Brian Jones --
I'll offer a suggestion -- might help, perhaps not.
You might create a second partition on the internal drive, but let it be APFS for now.
At the same time, have an external backup drive (SSD would be good), formatted to HFS+.
Use CarbonCopyCloner (or SuperDuper) to "maintain the backup volume" (instead of Chronosync, I would think).
CCC (and SD) can "work across the gap" of APFS vs. HFS+ without problems.
Do it this way, and you'll have a copy of your data (on the MacBook) that won't mess with the system, and an exact copy (on the backup) that can be connected to any other Mac.
Again, just a suggestion...
Personal experience:
Like the OP, I, too, prefer to keep "my stuff" on a SEPARATE VOLUME that is not "part of the boot volume".
I've been running this way since I had a Macintosh SE30 (1989).
No intention of changing, ever (I ain't got that much longer to go)...