A thought on In depth customization:

[Shougun]

In a lot of MMOs there is this concept of merit, FFXI being one of them, where you can spend that exp that would normally go off to die on things. It is nice to have stuff to keep growing with past the moment of hitting cap, but in this situation where it plays into stats it can often add a whole new issue when trying to group (like must have X merit points to join my ultimate party, or what have you). Edit: just to add for clarification I was speaking of merits from FFXI specifically, not OP (OP is pretty clear that it's not stat related, I'm just starting the beginning of the thought process with that as reference lol).

In this vein, with inspiration of FF sRPGs, I had thought it would be cool to have cosmetic merit system- inspiration being sphere grid, crystarium, and license board. With our soul gems one might be able to envision a soul grid UI dedicated to each job.

Your example with black mage, assuming it was just purely a visual example, would fit then there- something you could unlock for the heck of it. For Dragoon I like to comment on having a node of half fall damage that you can later upgrade into no fall damage, or the ability to unlock a higher jump than normal (given that you've unlocked flying in zone, perhaps by holding space bar determines if you go normal vs 'dragoon' jump). May also add exceptional cost opportunities like unlocking specific nodes for all jobs (like you might be able to unlock half fall damage for all jobs, no fall damage being an exclusive to dragoon though). The cool aura effect from HW for Dark Knight could be unlocked. Bard might have instruments cheaply put in there (more cutely unlocked than annoyingly, except perhaps adding a very expensive unlock for Otamatone lol), a mount that is the bard playing musical notes that float down to create the cloud they're resting on (with special feature of allowing them to use their musical instrument and mount).

Thought there might be a general category as well when you've capped out a job and want to move it into a generic area (maybe at a non-perfect conversion), could have things like different teleport effects - like more Ascian style teleporting, and other options (maybe you do a sort of Emet snap and you vanish). Like dragoon no fall damage you might have other non-instance specific impacts to the game that are generally more flavor (no fall damage in the open world is nice sure but it's not going to make or break balance in the greater scope of things), so if you wanted Alchemist might have a chemist buff that makes potions last longer and are more effective (working outside of the job, although may need careful thought on if that effects gathering related consumables).

On the changing of abilities out for other like abilities that get upgraded at the same time, it's not too bad to imagine, but SE might wince if it's something that makes them be held responsible to constantly update something separately. Like at a certain point WHM abandons elements, if there is an option to get the elemental effects back I would wonder if people would expect the merit for that gain upgraded impact effects (like Glare 4 at level 120 might be this epic thing, meanwhile if you use elemental switch it might be stone 3 still lol?).