Run PRAGMA optimize upon closing database connection #3745 reported a tremendous speedup, however you’d have to run 2.0.5.1, which also allows SQLite VACUUM from web UI Commandline.
VACUUM - performance improvement is huge
YMMV but if it helps you can make it automatic.
–auto-vacuum
–auto-vacuum-interval
It’s too late now, unless you want to restart the backup, but the –blocksize=100KB default may be smaller than optimum for large backups. It results in a whole lot of DB work tracking all the blocks.
Thinning versions can also help keep DB (and destination) sizes under control. –retention-policy.
I agree with @Ingmyv that getting this going at all should be done before trying to make it faster.