So Flatseal is used to harden flatpaks, not weaken them, normally.
that it would make my backups and restores take 900% longer and would rinse my data when they need updating.
You mean their storage space? Yes, biggest problem. Not very well solved tbh compared to android where all apps are also sandboxed but they have sizes of 30MB or something.
Flatpaks should be preferred over many other formats though, as they just work, dont touch the system and are more secure, unlike Appimages.
I highly recommend to watch this talk that some commenter mentioned