You’re brilliant - I think you have it figured out.
Do the modules you’re using look like:
as opposed to:
Note that in the lower image, there are two pins at the “front” of the module which are missing in the upper image. One of these pins is “DIAG” and if it is missing, then you will not be able to get sensorless homing working.
If that’s the case then you have to solder in the two pins or get a couple of TMC2209 modules from somebody other than Two Trees (which have the two pins already soldered in).
This is particularly frustrating for me because a couple of weeks ago I wrote:
Note that I didn’t include the Two Trees module as I haven’t worked with it.
Hopefully this is your problem and I’m sorry that it can’t be fixed in software.