Customization doesn't HAVE to be an illusion of choice. While it's certainly the case that the hardcore parsers will eventually work out what combos are optimal, so long as the variance in potential is small it won't stop them from participating in content. It's the same reason why (most) raid groups allow job variance: while certain jobs might be better for certain fights, they all do well enough that turning away, say, a MNK to hold out for a DRG is rarely done and considered petty when it happens.
The potential is there to allow deep job customization without everyone turning to the same cookie-cutter build, for precisely the same reasons that not everybody plays the same jobs in the existing game. The individual mechanics of each job appeal in different ways to different people. With a system of customization, different job builds would appeal in different ways to different people. So long as all those builds are viable, there is still choice.
The danger is that the greater the level of customization there is to be had, the more potential there is for a player to "screw things up" and wind up with a build that is NOT viable. To avoid this, there are three options: They could allow the playerbase to sink or swim, let the folks learn that they'll get nowhere with a nonviable build (FFXI did this). They could endlessly tweak abilities to try to keep everything even, or at the very least shuffle around which build was on top at any given time (FFXI AND FFXIV have done this). Or, they could reduce the amount of customization available, so that there are only a few builds to tweak at any given time (FFXIV's chosen path). The last of those three is the easiest, and upsets the fewest players - at the expense of creating a fairly bland playing field where everyone is pretty much the same.
FFXIV, ever since the disaster with version 1.0, has shied away from taking chances, so it's not surprising at all that they took the easy road. Options for customization have been getting fewer and fewer over time, and I expect that this trend will continue. It would not surprise me to see the whole Materia system disappear eventually, for example - though that one's so deeply entrenched in the game that it might be more effort than it's worth to remove, just to protect players from melding Spell Speed onto their Dsciple of War gear (it'll make my Ninjutsu faster, right???).