I think it's completely fair given that Steam doesn't give smaller games a realistic chance for the Steam Awards. I love RDR2, outstanding game, but a labor of love it is not.
Valve really needs to put it up to an industry/journalist panel that is supplemented by user votes or something. Especially seeing as Valve and Steam are one of the key players in the indie scene.
I think RDR2 winning that category is debatable, but in the end, Valve doesn't curate it, and it's up to the community to vote. I think your suggestion is good, but it's probably a lot more work than they want. Having the community decide has its charms but also major flaws.
If you want to talk about someone being robbed, Shadows of Doubt should have won Innovative Gameplay :((((