Not in my experience, I never had an issue and if you did have an issue with any site you can just disable content blocking for that particular site.Well if I do a clean install then I would just re-download any apps. I wouldn't just bring them from my backup. I would only bring over my files like documents, music or photos.
Some of the reviews on the MAS say that it blocks too many things. Plus it's a paid app with "in app purchases".
Additionally, it has no in app purchases as you claim. It simply says at the bottom Tip jar so you can donate IF you want. It doesn't pop up anything or nag you to donate.