Figured I'd answer my own question. I made two attempts to contact Apple Support and another attempt to post to Apple Discussions, with no results.
So I copied my entire iTunes library to a backup disk, and did my best at keeping notes at how many songs I had, which were what status, etc. I knew if things went south, I'd have quite a project in figuring out what songs to restore, but couldn't think of another alternative.
After I finished backing up, I loaded my original desktop iTunes library, and picked "Update iCloud Music Library".
It took about 90 minutes for 6,177 tracks, first analyzing music, and then uploading to iCloud. And the end result is that it looks like it resolved matters perfectly.
I've seen other articles from the past indicating that "Update iCloud Music Library" only led to partial success, and led to people doing long involved processes like opening a new library, deleting all their tracks there, and then going back to their original one to re-analyze and download, but to me that seems more error-prone and unnecessary.
Brief stats: Before I did the update, I had:
Apple Music: 2912
Uploaded: 2486
Matched: 8
After the update, I had:
Apple Music: 43
Uploaded: 3135
Matched: 2228
The rest of my songs stayed consistent in status (Purchased, Ineligible, No Longer Available, Waiting, Error). So far I don't see any songs that are improperly categorized, and all of my personal recordings are properly Uploaded.
I still don't know what would have happened if I had canceled, but matters seem improved now.
Best Answer
According to the support article for iTunes Match, tracks will not be uploaded to your iCloud Music Library if they:
The "quality criteria" include the bit rate, and I believe the same criteria apply with Apple Music.
You could try converting one of the files to 128kb/s or higher AAC format, using the start/end time settings in the track's Get Info before converting if it's longer than two hours and/or if needed to get the resulting track under 200 MB. If that track still won't upload then something else is going wrong.
You can always sync files like this manually. On older macos and windows, add these to your iTunes library and sync via iTunes.
One newer macOS - add the files to music or podcasts app and sync over USB.