claim that the device promotes pirating of the Amiga IP
If you mean the Amiga™ they are called mimimigs and if that fails then call them Amante :-D
threatens Amiga patents
If you mean hardware patents they have no legal case, reproducing the chip functionality without being an exact copy is legal, since AMD makes Intel x86 chips and how Intel makes AMD x86-64 compatible chips. There would be a legal case if the zorro I/II/III interface was used.
promotes piracy etc. though use of the kickstart roms and ADF files
That is why a floppy interface is so important, remember you can load the kickstart from original amiga floppies. not to mention the operative system and 3rd party software. If reading adf is litigious then do not include it, anyone can add it later on the same way people install
virtual floppy drive. Also, if the AROS kickstart is never created maybe there can be an "Amiga Forever, MMC edition" :-?
Imainge a container loaded with Min-Migs
If we are talking about a thousand boards then we are speaking of a big box. Also, at least for the time being this is an "open project" so it would be more difficult for Amiga inc. to get litagious actions when there is no corporation or company, just individuals; it would be a pain in the fenny to track a thousand names, addresses, etc.
they own that design and the tooling, you still have to tool your own case since the board layout of the Mini-Mig is not the same as the MSX.
AFAIK no one is using it and I bet the company that made the plastic molds would gladly produce a thousand pieces to whoever asked for them. As for the differing layout, remember it is really a piece of plastic with a bunch of wholes, I think there is enough space for an internal 3 1/2" floppy drive

A design that removes the need for purchasing the mc68000 would be better.
That probably would be difficult, getting a bigger FPGA is too costly and it would be difficult to add a 68000 software core and leave space to continue to add funtionality.
BTW, I am only speaking my mind, but I am no lawyer nor verilog programmer, anyone with indepth knowledge feel free to punch me into submission ^^;