Time Machine thinks the size of my backup is bigger than the source
I eventually resolved this, though I'm not sure exactly what the issue was. Steps I took:

Wiped and reinstalled the OS using a SuperDuper backup.
Initially, Time Machine then showed the 'correct' size estimate, but then quickly changed to the incorrect version again. At this point, it was also showing me a phantom Time Machine backup drive that I couldn't remove.
Now suspecting some corrupted settings, I switched to my admin account. Having wiped my SuperDuper backup to use as a Time Machine drive again, I tried to set up Time Machine there instead. Here, I could remove the phantom drive, and the size estimates looked correct.
I switched back to my user account, and added back my TM exclusion folders. Everything still looked good.
First backup completed successfully \o/

It's possible trying to sort things out in the admin account may have worked in the first place, without the full reinstall. I guess we'll never know...