welcome to the Forum and the Nook. And congrats on finding a 2nd way to force the Nook to use the internal Adobe reader to open PDFs.
All the deficiencies you listed for QuickOffice are correct. Sadly, the only other way we've found so far to bypass it is to password protect your PDFs. Then they'll open with Adobe, with all the functionality you are missing.
When the Nook App Store opens at the end of the month, look for a non-crippled version of QuickOffice to be available there... for sale. The (older) version they've had in the Android market for the past year already supports all this stuff.
Actually, if all the devs weren't busy hacking Honeycomb builds, I suspect they could find a way to update some manifest file somewhere on the system partition, which would tell the Nook to keep opening .DOC etc files in QuickOffice, but use the Adobe reader to open .PDFs. It can't be that hard, but no one has looked into it (probably just removing .PDF from the list of files that QO says it can handle would do the trick... then they'd all default back to Adobe).
Ditto - Congrats on finding another way.