I wonder how they are calculating that. I bought the bundle, told them to divide what I paid evenly between charity and the devs and told them to mark my contribution down as coming from both Windows and Linux (I run both and downloaded both versions of the games). I really wonder how many others did something similar to me and how that actually affects the the averages and OS totals.

I'm sorry, but charitable donations are totally irrelevant as an indication of how much users of a particular are actually willing to pay for a game--all of the people in the top 10 have paid literally hundreds of dollars each, a feat matched only by MMO subscribers. Many people jumping on this deal may not even care about the games themselves as such so much as being able to donate to a worthy cause.
As for the platform divisions, as cogadh has noted this counts multi-platform users as part of each platform, so those who dabble will end up all over the chart even if they favour one particular operating system for most gaming (especially if selecting a platform is the only way to get the installer for it--although I don't know whether that's the case), and those who already have some of these games previously (but are buying again for charitable reasons) may be deliberately selecting their platform(s) they didn't buy for last time.
Also to consider is that while "indie" games will work on ancient hardware the same is simply not true for many games in GOG's catalogue--especially those using DOSBox, which seriously taxes the CPU for the more advanced games. Those that have multiple systems and have designated one as the "gaming" PC (not resorting to dual booting) will inevitably continue to get heavy-duty games for Windows in order to get decent performance.