Thank you, Adam and Phil, for engaging with the thread here. I thought it would be beneficial to start a dedicated thread (with an appropriate title) so that other beta testers are more likely to find the conversation and join in.
Concerning collections setting:
First of all, will this be implemented for all sections that involve a collections setting (e.g. collections, compare versions, & courses)?
 will this be based on the collection name or on an internal ID?
No, it won't be the collection name.
I think it's good to have it based on GUID as a general rule because of the ability to rename an existing collection. That said, it happens relatively frequently that I end up with a "new" collection to replace an existing one rather than updating in-place. This, of course, would orphan all the related notes. I think it's important to have some way to relink those notes, whether that happens automatically or via a command.
If this was initiated automatically, it would be good to have a confirmation dialog that perhaps would allow the user to point to another collection. 
a disappearing note is more likely to be surprising and confusing for the average user. That is, I wouldn't want to "lose" my guide notes if I decided to change preferred Bible, or happened to have opened BWS from a different version, etc.
I think this concern applies to collections, as well and in my mind will be more likely to happen.
Incidentally, notes on a personal collection also complicates things for sharing. If you share a note that's anchored to a section with your personal collection it wouldn't be visible to other users. That is, even if I got a copy of your collection, it would have a new GUID, so your note wouldn't show up on my guide section.
I really think that the ability to "re-link" has to be strongly considered. Yes, for the case of sharing notes, but more importantly, IMO, for collection replacement reasons.
Concerning Word-by-word Section notes.
I'm grateful that we can add multiple notes per word in this section. I'd still like to see a verse-level note, however. My request from four years ago still stands:
In the word-by-word section there should be a notes field at the verse level (while keeping the word level). Notes entered on the verse level would be available to all versified resources, and notes entered at the word level would be visible in the Original Language bibles as well as all Reverse Interlinears.