That's actually a plus for both users and developers. GOG have high acceptance bar usually quality wise, so it makes each release more notable (i.e. they try to avoid the flood of low quality releases which no one can keep track of). So if you pass the bar - you are likely to get some attention, while on Steam your release can be simply lost in the noise.
I can't comment on whether the application process does require a windows version, why would you cut out 95% of the customers by not having one? See http://store.steampowered.com/hwsurvey for the stats.
You should notice that the full line there is "Your game must be able to run on Windows as a stand-alone application" which I took to mean that you (the developer) must package all the dependencies with your game. Steam would take the reputation hit if it distributed software like Linux does (dependency hell).
That's actually a plus for both users and developers. GOG have high acceptance bar usually quality wise, so it makes each release more notable (i.e. they try to avoid the flood of low quality releases which no one can keep track of). So if you pass the bar - you are likely to get some attention, while on Steam your release can be simply lost in the noise.