Ah, I though this was about the *.ST floppy image creation functionality in Hatari options dialog...
...and not the low level floppy formatting. Low level formatting uses the "write track" FDC command, which is not supported for ST/MSA formats as they store only sector content, not the additional track information (what's between sectors).
IPF format supports the required track information, but the external capslibrary, which handles IPC format doesn't support such writes yet.
Hatari's Pasti/STX format supports write track though. In that case a *.wd1772 file will be created to record the write track / write sector commands and act as an overlay of the STX file.
AFAIK it should work, but I've never tried it as it's a bit inconvenient and I've never had any need to test low level formatting programs in emulator.
PS. Floppy image formats supported by Hatari are documented in the manual: https://hatari.tuxfamily.org/doc/manual ... isk_images