Ok, bit of an update from me - for those who have the same issue with macOS Mojave (yes I know this is a Catalina post).
My issue was albums within folders in the Photos.app were not syncing, unless the albums were directly under the built-in "My Albums". ( and I was using macOS Catalina, all versions, including recent developer updates.).
After hours and hours and days trying different things, I went back to macOS Mojave. The risk of this was that I could do all this "reverting" back, and still be in the same situation.
I had 240,000+ photos and videos in Photos.app (stored within) and upon extraction manually, all these were renamed and a total chaotic mess.
1) I did a clean install or macOS Mojave, to the most recent date release,
2) created a BRAND NEW Photos.library on an external drive (as I normally would do).
3) used an application called GraphicConvertor 11 (amazing been using it for years), used this to fix my photo renaming issues, which took a few days to sort out.
4) imported all my photos and videos again however this time, I decided to host my images outside of the Photos.Library, so I have more control for the file structure so I made sure that "copy photos to library" was not checked .
5) after days of importing photos, I then used smart filters to sort my photos into albums and folder heiracy's as I would normally do within photos. I have left it a few days and left the computer and Photos.App open for sometimes 12 hours, at a time to allow photos to cache pictures and created thumbnails and stuff whilst I was not using the computer.
6) today, I decided to try and sync, however before I did this I backed up my iPhone 11 Pro Max, and did a brand new phone setup... I mean, no restoring from backup!!.
I just had my first attempt at syncing photos and it works. Albums within folders works.
the only thing that does not work as intended and this was happening previously, was, once I had synced for example , 1000 photos. and this was "complete" I decided to sync another album, and this process removed the 1000 from the photo and "re-sync'd the photos'. So, now I am doing all in one big hit as I only want 77,228 photos on the phone lol.
anyway, I know it's not the point, Catalina is what we want to work, but honestly, I won't be going back to Catalina anytime soon until some serious improvements are made. I am a bit of a geek, and when they announce a new operating system, I start to look forward to it, but... this was a complete destructible disappointment. "it just works" is a saying of the past.