While this likely couldn't happen without the publisher's approval, I don't see a good reason why that wouldn't be given since the publisher allows FL to publish the work in Logos.
Here's the requested feature: The NET bible has (as far as I can tell) three kinds of notes...'sn' (study notes), 'tn' (translation notes), and 'tc' (text critical notes). It would be FABULOUS of these three kinds could be toggled on and off with a single button.
For example, I'd love to have a window with the tn and tc notes showing but the sn hidden. I don't really need the study notes (not that they're bad, they are actually very good). But the content unique to the NET bible is the tn and tc notes.
Since every note in the text is preceded with a key (sn, tn, or tc), this shouldn't be hard to do in Logos. Wonder if the publisher will go for it?
(FWIW, I intend to write the publisher and see if they would be willing to publish a paper version with only the tn/tc notes on the page.) Here's hoping.