To answer your first question, programs where you interview may not even know where you did your rotations unless they specifically ask. Programs are able to begin downloading your application at the beginning of September. If you do your home rotation in July or August, you'll be in the middle of your away when your application is in (or at least when it should be in).
Transcripts should already be uploaded by September, and the Dean's letter will be probably written and transmitted (November 1) before your registrar even gets your evaluation back from your away. So there may not be any written record of where you did your aways. I know I was asked during interviews sometimes where I did my aways, but most of the time it wasn't brought up.
I think you can get great training anywhere as long as you feel its a good fit. And if you are doing both of your rotations at community programs, maybe you are telling yourself that you feel better at a community type place, so who cares about the bigger academic places? Follow your gut.