Yup, although the people setting bounties seem to be the Alliance, so it is possible that he new book by sight or reputation. I think, though, that he just intuited that he was more than he seems to be.
FWIW, I see the connection between the episode and the movie as less a direct one than an indirect one. More specifically, I get the feeling – and this is just my opinion, not something I’ve heard from anyone involved – that the storyline of the movie was inspired by the episode. I could imagine them looking at the episode and thinking “this would work really well to provide action to tie together the overall plot we’re looking to go with.”
But that’s just me.
I also have to admit that the Firefly re-watch and the recent arc have really helped me to overcome the sadness that I felt (and I know everyone feels) when one reaches the end and realizes that… there’s no more. That there’ll never be any more. It’s really rough, and just watching the material again and again never really made it feel any better to me. But talking about it on the 'cast and interacting with a lot of listeners via email about it and so on – that seems to have helped a bit.
One other thing that helps: I ran into another fan yesterday. It’s always fun to run into Firefly fans in the most unexpected places. And, of course, he and I both snickered when another person mentioned Janism. Browncoats imagine something entirely different when we hear that word. 
Not just you. When I walked out I said something like, “So, Objects in Space. Writ large.”