No, flattr cannot be used for in-app purchases. The idea behind flattr is that you voluntarily honor a podcast (or some other work that somebody has created and put online) by putting them on your personal list of people that will get a fraction of some amount you decided to donate at the end of the month.

The key concepts being "voluntarily donate" and "not a fixed amount", which differentiates flattr completely from in-app-purchases.

Apple was apparently uncomfortable with such a strange concept that it could not bring into line with its capitalistic mindset, and promptly banned it.

Sad to hear that Apple hasn't changed its mind on this front.