I had to change from auto finding/connecting the printer using bonjour to direct IP to get presets for paper size, tray, etc to work.
Old Intel Mac with v3.0 driver works fine on Sequoia as long as you don't update the driver and tools, but once you hit Apple Silicon with Sequoia all bets are off. M4 Mac STRUGGLES to maintain communication with the printer and every time I would try to switch to a custom paper preset from the printer, the print dialog would immediately change it back to letter and then the printer would error with a paper type mismatch.
Canon goes out of their way to avoid their customers so no help there. Just same driver download page ad nauseam. No way to even try back rev. Just nothing.
Made sure Canon software had proper local network access in settings, but this made zero difference.
Tried sharing from Intel Mac but same exact issue so it is pointing to Sequoia and Bonjour. Since it works on Intel/Sequoia this left Bonjour. Network traffic showed constant on/off comms between new Mac and Printer. Printer would switch between online/offline/or not even there every few seconds.
Took Bonjour out of the picture and switched to IP with LPD and communication issues stopped, and custom paper sizes and print presets started working immediately. I'm guessing Apple half-a..ed Bonjour.
Good luck with your issue and I hope this might help.