Just going to answer your questions. Sorry if already mentioned by others.

Quote Originally Posted by Hasrat View Post
So, first thing I'm noticing, the Brand of ______ skills are kinda clogging up cross-class abilities now; are they ever particularly useful at this stage? I don't think I've seen any end-ARR crafting that needs them, and I get the impression that by using all the more useful skills, I won't really miss the lower efficiency even if I there are any, maybe?
Leave those skills off of your bars until you get a recipe that actually requires it. Until then, don't waste your cross skill slots on them, and when a recipe that requires it comes around, swap it with your least useful cross class skill.

Quote Originally Posted by Hasrat View Post
Actual skills:

Comfort Zone. Obviously I've seen this all over while checking things out. This seems like the skill to have up at all times? Unless I'm getting low on CP and don't have the time to wait for the recharge. But, near as I can tell, other than that, never a reason not to use?
You definitely only want to use it when you can utilize all of its stacks. Basically look at comfort zone as +14CP as that is what's returned to you after absorbing the initial CP cost. This means you should basically start your rotation with it always when performing difficult crafts, or at the very least, before you start using CP.

Quote Originally Posted by Hasrat View Post
Piece by Piece. Straightforward 45 CP to finish a craft. Sounds maybe useful if I guess I don't have the durability for anything more and I guess absolutely need those 3 turns to finish it? Idk. This one sounds a bit on the useless side, unless there are some really hard crafts somewhere that this will be my best option for progress. But much like the Brand skills, I can probably get away without it?
Actually, could it sort of act like a replacement for the Brands? Does it ignore elemental affinity? That could be cool. Still not very useful, but maybe a little cool.
Two non-specialist abilities increase progress by 33%: PbP and Muscle Memory. The thing about MM is you can only use it at step 1 of a synthesis, but is 100% success rate, while PbP can be used at any point with a reduced success rate. Remember to read the tool tips. It increases remaining progress by 33%. So it is the most useful at your initial progress increase. If you use it after, there is a high chance the progress will be even less than a careful synthesis 1. I cannot tell you if it ignores elemental affinity as I've never tried.

Quote Originally Posted by Hasrat View Post
Ingenuity (1 and 2). Literally never found a use for these. They do sorta sound like they could be useful, but it's just not very clear what "lowering recipe level" actually does while crafting. No idea how best to utilize this anywhere. Is it useful for improving quality, or progress?
For this, I am going to task you with something. Actually three. Pick something to craft that is currently one level above yours and right down the progress from Careful Synthesis II. Then I would like for you to do it again with the same item when you are the same level as the recipe. Then one more time when you are one level above it. Make sure you use the same equipment during these crafts. You will notice a SIGNIFICANT increase in progress when you are one level above the recipe, and this is what Ingenuity 1 and 2 are for. Basically ingenuity 1 for same level, and ingenuity 2 for recipes higher than your current level. The less progresses it takes to complete a synthesis, the more durability you can spend towards quality.

Quote Originally Posted by Hasrat View Post
Byregot's Blessing. This one seems a bit weird for me. A bit situational. There are times when I need the bit of extra CP from Rumination. And obviously I don't want to blow my Inner Quiet too early. So far, I've been looking at this as my Excellent skill. As long as that doesn't pop too early, can make some massive progress that way. I suppose I could also be using this when I feel like I've got quality close enough that it would finish off, but I'd hate to guess wrong and still be short and also no Inner Quiet so slower gains, and also need to balance that with any CP I might need to finish progress. I feel like keeping this skill is good, but I haven't figured out where it best fits in.
BB is your ace card. It also stands for bread n' butter. That's exactly what it is. With enough stacks of inner quite, BB can take your quality to 100% from a very low number, and even lower if you get a modifier from 'good' or 'excellent' status. Basically, you need at least steady hand 1 up and 56 CP to use both Great Strides (32CP) and BB (24CP) combo to finish your quality with enough durability to finish the synthesis. This is why it is so important to get inner quit up at the start or near start of your craft.

Quote Originally Posted by Hasrat View Post
Reclaim. Ehhhh. At this level, definitely feels like a waste of a cross-class slot.
Sometimes the decision is made to purposely botch a synthesis. Typically this decision is made when you have valuable mats, and nothing short of an HQ craft is acceptable. Anytime you are using expendable mats, you can forego crossing reclaim. However, when the important ones come around, you will be very happy to have this. Cross this skill when that time comes, and use it when you have a streak of failures that make HQ next to impossible.

Quote Originally Posted by Hasrat View Post
Waste Not 2. Basically +40 durability. But only if you're using solely Touch or Synthesis skills. This feels a bit lossy compared to Manipulation or even Master's Mend. I never really even used the Waste Not 1 unless I let durability get too low and needed a little longer to finish.
Another crafter will have to answer this for you. What I can say is Waste Not and Waste Not 2 are kind of commitment skills. Meaning that when you use them, getting good/excellent condition procs will force you to make a decision to increase quality/progress, or sacrifice it in favor of CP. This can be stressing unless you commit to using all of its stacks towards quality/progress. The reason why I don't use WN2 is because of the longer duration of this stress.

Quote Originally Posted by Hasrat View Post
Careful Synthesis 2. Straightforward replacement of the first skill which I basically never need again. At this point I could probably be getting away with using better Synthesis skills, but, I do like the reliability.
Yup!

Quote Originally Posted by Hasrat View Post
Innovation. This one feels a little tricky. I don't know if I could ever fit it into the 40 material crafting without wasting a stack. Crafting bigger things, maybe. This feels like it's best held back until you've got a few Inner Quiet stacks already, to buff the buff. But I also have trouble sometimes getting all my other buffs to line up just right to give me 3 clear turns, and I suppose I shouldn't worry too much if I lose out on any ToT usage, the bonus Control on top of a Good would probably make up for it. Like Byregot's, another one that seems smart to have, but not necessarily used for every craft.
You are correct, it is a little tricky. There are multiple ways this skill can be used, and each of them requires an abundance of CP otherwise that CP is better spent else where. I can tell you that the only time I really use it is in the middle of my GS+BB combo. If I will still have enough CP to use BB, I will use Innovation to 'fish' for a good/excellent proc. If I don't get it, at least it still has a modifier, albeit a weaker one.

Quote Originally Posted by Hasrat View Post
Any tips for what to do with some of these that I might not have thought of? If it matters at all, so far I've been using the Inner Quiet-Steady Hand II-Hasty Touch-(Tricks of the Trade) method with pretty good results. But with the 1- and 2-star crafting I'm hitting, just want to be sure I'm not wasting some of my skills that could be helping more than I realize.
It will be important to use these skills in combination when performing difficult crafts, and this is when people start seeking out rotations, but really all one really needs to know is how the skills work (read those tooltips), and using freehand crafting to determine the next best skill to use based on the current situation. This will get you the most success throughout your crafting career.

Hope this helps, and good luck out there!