There are some slight disadvantages of a smaller drive.
The time to restore from backup will not change depending on the drive's size, only on the quantity of data stored on it, subject to 2. below.
Smaller drives get full more easily [obviously] & you can't upgrade the drive on a modern Mac, so you'd have to use an external.
Full drives are slower to ...
All the things you list are user data and settings that the macOS upgrade and update and reinstalllation process will leave alone.
Time Machine has a compare feature where you could generate a delta between what is on disk and what the last backup interval saved.
Find Differences between Time Machine backups
Basically, Data is what you did to change the ...
If things are sketchy, what prevents them from infecting your TM history as well?
More secure options
Test things within a VM (ideally without shared drives etc).
Make a full-image backup of your Mac, make sure you can restore it and then unplug the backup drive from your Mac. Once done with the tests, wipe your Mac and restore the backup.
Get a separate ...
The sidebar will forget those mounted network aliases every time it can't find one.
The 'fix', although a bit clunky, is to mount the remote drives, directly alias them on the desktop, then move the aliases somewhere permanent.
Then they never break.
Backblaze might be a good option to mirror your entire Photos library. A 450MB overhead for a 90GB library isn't much; you'll need the database to fully restore your Photos Library i.e. albums, non-destructive edits etc. If you really want to backup just the original unmodified versions of photos and don't mind losing the organization and edits, you could ...