no, it's not just because of the guitar thing ... the question is, if Thom has a side project and he does the exact same thing as with Radiohead, then why is he doing it? you can give me tons of reasons, and they'll all be ok, but it will always be weird... but i'm glad that until now, this song is the only one that sounds VERY Radiohead-ish, the rest are different (more "electronic" if you want), even though it's still RH's singer (it's difficult to separate both bands). In a way RHish songs are a lot more safer with AFP, but i believe that's not what he wants to do with this side project, 'cause normally you make a side project when you want to do something different from your actual band.
I still like this song, don't get me wrong!