i do backups of my home folder with Vorta, tha uses borg in the backend. I never tried restic, but borg is the first incremental backup utility i tried that doesnt increase the backup size when i move or rename a file. I was using backintime before to backup 500gb on a 750gb drive and if I moved 300gb to a different folder, it would try to copy those 300gb again onto the backup drive and fail for lack of storage, while borg handles it beautifully.
as an offsite solution, i use syncthing to mirror my files to a pc at my fathers house that is turned on just once in a while to save power and disc longevity.
If i got it right, flatpacks gather all of the dependencies of the package and bundles them with tha package. Maybe those extra 290mb were from dependencies that you already had installed but that flatpak wanted to install another copy.