What if I have bin/app and I want to write separate documentation, should I place it in bin/app.pod or lib/app.pod? I'm thinking bin, will this make ExtUtils::MakeMaker upset? Looks like no. Is it poor practice?
It should be lib/app.pod (would conflict with App.pod, App.pm), but you don't have to worry about that if you include the pod after __END__ in the exe.

Is it poor practice?
Its very rare, AFAIK only perldoc does it, so I would say yes.

Maybe I should just place all my docs in a different dir structure?
No :) Ok you can do it, but then you have to make sure ExtUtils::MakeMaker::WriteMakefile() gets the right combination of arguments so they get installed in the right spot. I wouldn't bother.