Actually, attributing numbers to a class to find out how much they're worth is exactly how it works and anyone who can't see that is just being blind to how raid contribution works. More specifically, find out how much they contribute by existing. DPS "belonging" to someone doesn't even matter if you don't agree with where damage belongs to; the fact is, you do more party DPS because you have a BRD or MCH in your party, personal DPS be damned, and you have to take that into account in ranged strength, much like how DRG is "worth" much less if you don't have a BRD/MCH in the group for it to not contribute as much.
In your example, if you were for instance farming with said NIN who's doing garbage, and you had a rep who's ready to come in, you can easily say "Well our group DPS is poopy 6,000 DPS with this terrible NIN, he's only doing 800 DPS; I've got this crappy SMN friend who will come in and do 850 instead if we want, but looking at the NIN's contribution of his 800 + Trick Attack + Shadewalker he's worth about 900-950. Then again, I have this DRG who can come in and do 850 but he'll buff all our ranged by 7-9% with Disembowel and add about 2% to the group with Litany ... he'd be worth an easy 1000++, let's go with him."
Also, PF is deadly easy in this game. What are you PFing that a 2 ranged comp is holding you back on, A3S? For reference, when my group would sell Thordan, we took BRD + MCH a few times in a 7 man and did just fine, miles before any form of enrage would happen in any phase of the fight (clearing immediately after the ice + ground AoE), it's just L2P, absolutely nothing to do with balance. Any 8 man group in any content Thordan or easier should be able to run any comp they desire, the only thing holding people back is skill.
The game should not be balanced around PF success with random comps. PF groups have the same opportunity to create a comp that's optimal just like real raid groups; if they create a group that gets filled with BRD BRD BRD MNK, that's the party's prerogative. The issue would be if comps are literally unable to clear old/easy fights without a specific comp, and I am positive nothing below Savage raiding requires any specific comp to work.