When homing Y, it moves about a CM and stops, then call itself homed. This obviously doesn't end well. I tried tinkering with the Y axis homing options but no reasonably close values get it to home reliably. I've found it seems more likely to home on the second attempt, and fails more frequently if X is centered (so often I'll home X first, then Y). The printer prints fine once everything homes correctly, though one of the motors seems to be significantly louder than the other (the one next to T0) Ideas?
Not really. You might want to read about some of the adventures of @orcinus https://forum.e3d-online.com/threads/c-axis-sensorless-homing-works.3303/. Personally I've reverted back to the stock ones, but have also had the odd Y homing incident. Now, when the machine comes on, I tend to home Y manually before anything else. I don't feel 100% confident with it though. I've since built the homing and bed levelling into the print startup process, so I simply watch it home at the start of the print. If all goes well, as you say, it's fine once homing completes. But I want to keep watching it for now. The real 'fix', as such, would be a physical endstop similar to the Z endstop.
Try reducing the sensitivity a bit to S3. That will definitely be much noisier, but so far, i had 0 failures at S3. Another thing you can try is increasing the homing speed a little. And yet another is to wiggle it a little before attempting a home.
There's a lot of usefull info about sensorless homing on the Duet Dozuki, sensorless homing sometimes needs some finetuning.
I've also changed to S3 and can report no issues other than the one that made me have a tinker! Incidentally, I've also changed all of my macros to pick up tool 0 (only one tested so far) at Y=242.5 (rather than 242 of the std settings) and had no more of the dropping tool issue that made me up the sensetivities.
I only just spotted that yesterday when I had a random tool drop and also changed all my pickups to 242.5.