The reader side and corresponding LCD side interactivity are three apps that enTourage has written/customized, namely the Reader, the Journal, and the Library apps. Rooting will not affect these. Changing the OS will basically mean you'll lose these and any apps that enTourage has written/customized themselves if the existing binaries aren't compatible with the new OS, including the drivers for the eInk side. The eink display will remain available to you as a second monitor, although you'll probably need to acquire/customize the display & input drivers for it (much like robot did in his experimentations).