If you have read the patent then you should have noticed how the data separator works, and that it is setup to handle flux data and that's it. You send/receive pulses, and those are converted directly into either a MFM or GCR data, depending on how you have Paula setup. If you know anything about MFM you would know that there only certain combinations of bytes that are valid, and all other combinations are not decoded or encoded correctly from a series of pulses. It doesn't matter what provides the pulses (magnetic media or a clocked line from a microcontroller), the end result is the same.
The HRM does not go into the internal workings of the disk controller, but instead discusses the MFM/GCR modes, 2us/4us modes, etc.
You can believe what you like. I created more than 60 commercial disk copying related products for the C64 and Amiga, so knowing the exact functionality of the disk controller hardware was my daily job.