It depends on what angle you are looking at.
The price of the wargear will not change ingame, so a set price makes some sense if you consider points an representation of amount of influence/money.
As you mentioned some models can make much better use of it then others, so ingame balance asks for pricing dependent on usefulness.
I agree that the norm is that the piece of wargear costs the same everywhere. As long as the variations are limited it does not matter much, as you mentioned the base cost factors in part of those prices (why is a base archon so expensive compared to a base warrior, 7 warriors will kill the archon all the time). The disadvantage is that some upgrades are rarely worth it since they are to expensive for their output (have yet to see any warrior squad with a splinter canon). In other cases it means that buying the unit is more like a delivery mechanism for the options, you buy 5 guys but actually would be happier if you could have the 1 guy who carries the special weapon.
I personally think that wargear based on individual options has some merit. Unfortunately it also introduces a lot more variables, making for even more lines of paper and possibly with unintended side effects, with limited gain. What I do think is that for different codexes a different price might be in order.
Consider 2 imaginary codexes:
Army A has no high ws/bs characters (they give blessings to booster morale, but suck at fighting).
Army A is based mostly around faith, Ws and BS is 3 with a few exceptions of 4 and an almost universal str of 3 and 1 attack but most have fearless. So let's say that only their faithmakers (ws s 3 and 1 attack) and a melee unit with rending (also ws3 s3 and 1a) can take a power sword at 5 points. The option is there sometimes it will be taken (it is only 5 pts), but at means 1 attack with rending or 2 at the charge the gains of ap3 are minimal.
Army B is highly elite (ogryn sized) has at least 3 attacks base ws 5 and str 5 and multiple wounds across the board, the base cost is higher. But the base cost cannot be so high that it would invalidate them without some special weapon or they would be useless, but giving all those guys power swords for 5 points would also be insane. They gain at least twice as much from the power sword, especially because they do not rending and thus "need" it more.