It's because the NOOKcolor has a special QuickOffice viewer for PDF's without DRM. If you sideload a DRM'ed PDF then it opens in the regular Book Viewer and you have the additional features below:
PDF's viewed in the Book Reader:
Searchable; no landscape; can select text font size but can't change background theme color; change pages by swipe left or right (or tap); shows book name on top bar across screen; table of contents viewable; bookmarks with selectable list; no annotations; no dictionary; remembers last page read
It would be nice if you could select whether a PDF opened in the Book Viewer or Quick Office. Here is an old thread with a similar discussion that may interest you.
https://www.mobileread.com/forums/sho...d.php?t=104764