I had a original nook which had truly awful software. Even the library function where you select books was truly painful to use and couldn't even search both books you had downloaded and those you had paid for electronically so I jailbreaked it with a tool that relied on loading a url with an exploit in its browser and gained in addition to a library app that worked everything from a twitter client, to dictionaries, to pandora.
Ultimately the functionality didn't interfere with the built in reader software or OS because it was entirely orthogonal the extra functionality was more icons on the launch screen. It didn't need the developers to create much in the way of extension points save for the expectations that the launch screen wasn't hard coded but rather it would let you select from whatever apps were installed. Something pretty common in basically every OS.
If your work doesn't have some degree of natural separation between A and B I don't know how you can possibly have made it work in the first place.