Hello and welcome to paper2d family!
If i understood correctly you are having problems making collisions work with flipbooks? If yes you must activate collision option within flipbook .It is a common misunderstanding that since you have collision for every sprite then flipbook that contains those sprites will have them as well as default.
Collisions do work with capsule components as long as they are in a different collision channel, otherwise all sort of funky things start to happen.