Agreed about challenge being required. I don't think they can make all of the highest level crafts challenging though otherwise there'll simply be a huge drop-off in crafters after a certain patch (can look at ARR as an example or HW after favors came in). But they could always release two versions of a similar item: one with a slightly lower item level but easy HQ requirements and the other much harder craft with things like higher item levels and extra meld slots or something. They could use the same item skins so that they don't need separate gear designs.
The only truly difficult crafts released so far have been the master 2 tokens from ARR, but I don't think we'll be seeing anything like that again anytime soon anyways. Those are the only crafts that they've released where 11 stacks of IQ alone did not give you anywhere close to enough quality for a reliable HQ. In fact, you generally only got 30% unless you did one of two things: baited for a good proc (semi-reliable) or pushed additional touches. One extra touch beyond 11 stacks gave you 50-60% depending on your control and 2 extra touches gave you 70-80%, all while landing Byregots on normal. That's why freehand crafting was so important. Using the popular 2 RS and 10 HT rotations around that time, it was a 15% chance just to build 11 stacks of IQ and you put yourself in a position where it was impossible to get >30% without baiting for a good. However, freehand crafting could give you 11 stacks of IQ possibly up to 50% of the time and often eliminated the need for proc baiting (made baiting a bonus to get an even better result).
Whether Maker's Mark dies or not will depend on the tuning. In HW, Maker's Mark was the best method because you could clearly tell that crafts were tuned around it. The only way to get the required CP to craft from 0-100% reliably was if you went through all of the FS baiting steps. On average, you got just enough CP for that 0-100% run.
A 50 step synth is longer than a 30 step synth, but for the 30 step alternatives, you likely had to run it multiple times to HQ some intermediate materials, particularly for the i250 weapons where even individual crafted 4* materials did not give you that great of a starting quality boost.
I think that in the future when progress requirements becomee higher and higher, they'll make the appropriate adjustment to flawless synthesis or introduce new progress skills to replace all of the current options.