Amiga disks use MFM, but don’t use IBM scheme. Instead, the entire track is read and written as a unit, with each sector butting up against the previous one. This saves a lot of space which allows the Amiga to not just store 880kB on a DD disk, but also allows an extra 16 bytes of metadata per sector.
Bizarrely, the data in each sector is stored with all the odd bits first, and then all the even bits. This is tied into the checksum algorithm, which is distinctly subpar and not particularly good at detecting errors.
fluxengine read amiga
You should end up with an
amiga.adf which is 901120 bytes long (for a
normal DD disk) — it ought to be a perfectly normal ADF file which you can
use in an emulator.
If you want the metadata as well, specify a 528 byte sector size for the output image:
fluxengine read amiga -o amiga.adf:b=528
You will end up with a 929280 byte long image which you probably can’t use in an emulator; each sector will contain the 512 bytes of user payload followed by the 16 bytes of metadata.