Yes, different readers will probably be MORE compatible with your .epubs w/o messing around with covers.
Although rooting won't mess up your shelves; if you use a different reader, your shelves for the B&N reader will be meaningless. So I wouldn't spend too much time on those if you thing you might end up w/ a different reader.
I read my sideloaded .epubs w/ Aldiko; and my B&N purchased content w/ the B&N app. Although I generally remove drm; I enjoy the convenience of the B&N reader for content purchased from the B&N store.
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