Migration Assistant won’t copy (some) files, though running through smoothly without error
I want to commiserate because the exact same thing happened to me after using Time Machine to restore my drive recently after I put a new SSD in my older Macbook. The restore took a good amount of time and seemed successful according to the UI however I noticed that exact 2 folders you mentioned hadn't been restored. (I didn't notice anything else missing.) So I manually copied the contents from my backup and went along as usual...
I ended up here however with a new issue; for other reasons I ended up getting a new machine a short time after that. I set up the new Mac using Migration Assistant with my Time Machine backup, which seemed successful this time. (all folders appear OK, although my Plex Media Server app database seems to be corrupted now).
My big problem now is that I went to restore that particular file from Time Machine, and see that I have no history  dating to before the migration! I looked at the backupd folder for Time Machine and it's now got a new folder where the new backups are being made named &quot;my username 2&quot;... the migration somehow forked me into a copy of my username, making my backup files longer accessible to Time Machine's UI. I probably should post my issue here separately... I also have no confidence now in Time Machine.