The problem lies in both, the designers, as well as people who insist on conflating ability selections, which by definition are strictly a mechanical component of the game, with their "RP".
I’ll admit, this was probably one of the harder things to get right in my own system. My ultimate solution was just to minimize the fluff associated with the mechanics down to literally just a pithy name for the ability.
For example, one ability that can be selected is called “Nothing to See Here” that lets you use your Presence stat in place of Reflexes for Stealth checks (which, depending on relative scores may be superior to gaining skill with Stealth or which might be stacked with skill in Stealth to allow an otherwise mediocre reflexes PC to be good at going unnoticed).
How does it work? Well, that’s up to you. Maybe it’s a Jedi mind trick, maybe you’re just really good at looking like you belong so no one pays attention to your walking down the hallway. The mechanical part is fixed, the RP is up to you.
The same goes for combat abilities; there’s a combat talent called “knock them around” that allows you to shift opponents you hit or knock them prone if you hit; but the how really depends on your character; a human might sweep the leg, a Minotaur might head butt them, a sprite buzzes around to throw them off balance, a dragon follows up its hit with a smack from its tail. Regardless of the RP reason, your PC is really good at knocking people around.
Sure, some things are harder to justify in multiple ways than others, but those are often very specific abilities you’re taking for a specific reason and, since there is no big fluff blurb attached to it, you’re usually taking it purely for the mechanics.
A similar hurdle was to just make it really hard to accidentally mess up a PC. This resulted in a lot of baselines just being hard-coded to not rely upon or minimize bad choices.
The basic to-hit bonus with skilled weapons, for example, is Strength+2 (min. 5). Unskilled weapon use is just Strength and has no minimum and Strength can range from -1 to 5 so, as long as you’re using a weapon you’re skilled with you’re hitting as if you had a 3 in Strength (damage will be less, but level bonuses to damage will eventually minimize the difference).
You would literally have to both tank your strength and use nothing but weapons you’re not skilled in to be completely useless. Even if you somehow accidentally started in this state, you could mostly fix it just by switching to a weapon you’re skilled in so the ONLY reason you could ever see this in game is if the player just wants their PC to suck.
Nothing can stop deliberate gimping, but I feel fairly confident in saying that my system has enough tools available that concept/RP should never have to be sacrificed for baseline mechanical effectiveness (also, because of this heavy optimization will also only yield a 5-10% performance increase over the baseline... enough to be an award, but not enough to completely eclipse everyone else playing either).