Jeff, good to see you here.
The HxC is a wonderful device, and for most normal and many abnormal floppy formats it works extremely well. I have one set up with my REH CPU280, and it works perfectly. I recommend the HxC emulators any time the subject of floppy emulation comes up, since they are that good.
However, the TRS-80's can have some really abnormal density mixtures thanks to their use of the Western Digital 1771/1791-derived floppy controllers. The 1791/1793/2793/2797 are capable of mixed density operation within any single track as well as on different tracks; I have disks that have both MFM and FM sectors on the same track, and on more than just track 0; with these controllers it is possible to have essentially two half-tracks on one track, one half FM and the other half MFM, with overlapping sector numbers, even. David Keil's DMK format acknowledges and supports this ability. I would like to see a discussion of HxC true intermixed density support; what would be the best place to do that? Over at the HxC forums?
Now, back to the Model II's boot track, what at least one of the TRS-80 Model II operating systems, LS-DOS 6.3.1, does is actually format all 77 tracks to MFM. It's only when you backup the system files to a disk that it re-formats track 0 to FM. This makes it a bit difficult to pre-make the disk image, since the FM support to track 0 needs to be automatic and dynamic, following the controller. But I understand it's a bit difficult for the drive to know what the controller is doing, relative to FM and MFM, especially if the encoding is changed on-the-fly (which the WD controllers are able to do, and TRS-80 operating systems and utilities actually do in practice).
Just looking for some ideas for the already great HxC to be a little better, at least from the TRS-80 side of things.