100% you have to think about that when going about it but also that does not prevent SE from being able to do something with it (like our gender locks or summoner egi).
Actually let's take Kazrah's idea of making magnetism a big part of Geomancer, how could we do that fairly smoothly?
Well we just had a new dimension open up- what if in that dimension we had a Geomancer related job that had discovered the ability to manipulate gravity/magnetism at such a level that makes other jobs pale in comparison (these guys are amazing at it), then one of the mages from that other dimension travel over to ours to find interesting elemental variant of a type of directional magic they use and they get together to influence each other (much like AST and GEO did). Not only new skill sets for our side but could also introduce new skills sets as they work together (like if we use super compressed magnetism and earth magic we get a sort of magnetic fire, now Geo has fire spells!). Here we could also use the new outsider as a source of civil war in the Hingan Geomancer school too even, adding to some fun lore value to doing the quests (your school is falling apart and later you have to help it rebuild while fending off an opposing faction of Geomancy). Side note Gravity is a AST skill so of course the names will have to be Geo related, like how Red Mage can use fire but it isn't simply given a black mage fire name (I mention gravity here because magnetism on an enemy to the ground would probably have the feeling of being a gravity based spell).
Okay so now you say "well enough but what about all that AST/GEO content it'll not be right... right?", which I would say there is a sort of chronological order to the quest SE has already done/accepted in the game (time/echo have given a lot of quests leeway). For example you can help prepare the meal that Nanamo has in a MSQ that you've already completed (as part of another job's quest). GEO the job would start after the first opening of another shard, while GEO of Eorzea starts before that - it's not an issue. Of course having to wait for the shard concept to be available would push the job's starting level to like level 70 but I suppose that's only an issue depending on when the job is introduced. Also I want to say this was only one very quick possible way to make them work without retcon (get the lore team at the table to solve this and I'm sure they'll find something that checks all the boxes they need, if they wanted to/were told to at least lol).
Back with summoner people would say "no way you can have a fancy egi because of lore" which was true that there was lore that explained why our egi were small and controlled, but the issue was people using "lore no" didn't account that you can always add more lore if you want to make something work. Or maybe in their defense simply meant "right now" but of course when adding new spells/jobs I think it is better to think future forward as in that time new lore will exist (and so the issue of lore becomes no issue as every time you get a new job / new skills that lore is added to the game anyways).
To spin this on a greater issue that's more important to people. The lore in the past which was removed (shifted) and the lore currently for Viera and Hrothgar have been used for genderlocks. If you accept that lore is fixed and unchanging, that we can never add something to make Geomancer work, then I suppose it should follow that we should never unlock Miqote, Highlander, Roegadyn, Viera, or Hrothgar. Or alternatively if you see that "well we just need some more story that spins it in the right way" to unlock the genders, then it should follow that given enough spin you could do the same to Geomancer. That's why I said a lore lock/no is only as strong as one's lack of desire or creativity to solve it, and having seen what the lore team has done so far.. They do not lack creativity to make something happen if the team wants to do something. Meaning the lore team has our backs when it comes to evolution of the game (although we should still strive to avoid retcon, that's not so good).