Was trying to make an origin that uses experience points as a resource and such, but this threw a wrench in my plans quite solidly after I realized what was on the documentation. :<

Can this be changed or was there a particular reason points couldn't be subtracted? because it's likely to make the costs of my origin's skills too steep at it's higher levels, and commands can certainly subtract xp points. but I'd rather not be running commands on the player constantly.

As far as I'm aware, no other reason than fabric did it this way. Minecraft's code is capable of handling both as far as I'm concerned.
I mainly aimed for the least amount of modification to the code in 1.16.5, so I didn't change this.

As for running commands, if you about 1/s there shouldn't be much of a performance hit.

well alrighty. and yeah, there isn't too many going on. but they're kinda sporadic:
a command per 700-200 ticks doing food restoration.
one on a cooldown between 140-60 on attack,
one on another similar length cooldown based projectile power
one on death on or above level 30 and with 1000 points available
one every second during a toggle active. :V

The last one might cause some trouble on a server with multiple people active.
I am currently not adding content to 1.16.5 and trying to fix things while I wait for Mixin in 1.17, so I won't add that right now.
I'll probably add it for 1.17 though, and you might want to report a bug on either origins-fabric or apoli since it could be useful for both versions of the mod.