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Let's see if I can clear things up - and not make the water any muddier!
The stock Nook reader can open books that you've purchased from B&N (of course) and downloaded with the stock reader. It can also see and open ePub books sideloaded to that 1 GB partition. The stock Nook reader cannot see or open any books you might put on that B&N partition in any other way (e.g. Calibre Companion). To read those books, you need to install a compatible Android reading app - preferably, one that plays well with eInk.
If you install a launcher and apps, your installed reading app(s) can find and open any books you've loaded on the B&N partition. These apps cannot find and load any books you've bought and downloaded with the stock Nook launcher/reader. These apps cannot access any books on the 1 GB "sideload" partition.
Ergo....
To access your stock Nook books and any books sideloaded on the 1 GB partition, you need the stock Nook launcher/reader.
To access any books you've sideloaded with Calibre Companion (for example), you need to launch your installed launcher and open your installed reading app.
Now, everyone has their favorite Android reader apps. I find that, overall, AlReader works best for me. It also has an eInk mode, so it looks good on eInk. Moon Reader is good, but doesn't look quite as good on eInk. If you use the Outdoor theme, however, it's pretty good. Either can easily find and open books sideloaded with CC. Each has its strengths and its flaws, but either will do a good job.
With root, it is possible to find and access the folder where the stock Nook reader stores your downloaded B&N books, etc. However, I am not messing with it. I assume that the Nook reader is set up in a certain way, and expects its books to be in a certain way. I do not intend to give it indigestion!
And yes, you can choose between Nova Launcher (or any launcher you install) and the stock Nook launcher - every time - unless you choose one as default.
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