I had a little time to test this today. And with my TF536 fitted in my A600 with KS3.1, I have no issues with my internal floppy. I can read disks in Workbench, and can boot off them fine.
Only one disk didn't boot and that was my backup Workbench disk that I used to use and has been heavily abused. Doesn't boot but can be read in Workbench fine when booted from another disk or HDD. Original workbench 2.05 disks, AMOS, DPaint, Octamed and various magazine disks all boot as expected from DF0