We've had this discussion year-in, year-out. On one hand, the whole point of video game music is to support the medium, that being video games, hence it really should be judged in context of how it works in the game. On the other, it's also completely possible to judge music on its own merits, whether it comes to composition, production values, how it works standalone, etc. And it really isn't possible to expect any one person to have played every single piece of entertainment released in a year.
I don't think GAF votes have had any clear guideline saying you have to have played a game to vote on its soundtrack, but it also is generally what most people gravitate towards when voting, hence it does turn into a popularity poll of sorts, with more niche games getting 'overlooked' just by sheer fact you can't make up that number of warm bodies.
I mean, yeah, bemoaning the fact Cold Steel 2 isn't represented is fine and all, but it is what it is. What does amuse me though is when people bring up niche titles being overlooked, when they pretty much fall into that same issue of essentially being out-of-sight, out-of-mind, just with different titles.
There's a lot of good music out there to be discovered. Always has been, always will be.