The S100Computers web site provides an impressive range of modern-design S100 boards. There is however a considerable amount of untapped potential for what can be done with those boards, in terms of software development.
Re the 68K boards. CP/M-68K is available. Cromemco CROMIX was ported to the 68030 board thanks to the considerable amount of work done by one individual and documented here:
https://github.com/dwildie/cromix-s100computers . UNIX has not been implemented for the S100Computers.com 68030 board set. There are no "new design" or reproductions of the Cromemco dual Z80/68K CPU board.
Re "is it common for folks to have multiple CPU boards in one system". The answer is no. I have followed the discussions on the S100Computers Google Group for a long time, and based on discussions there it is my impression that at most a few dozen hobbyists have completed a build of more than one (let alone several) slave CPU boards for their S100 systems. By far most of the interest remains concentrated on systems running "only" a Z80-based CPU.
Re FDC controller. As you noticed, there is an FDC board in the S100Computers.com board set. Again, my impression is that only a few dozen of these boards have been built. System software support for this controller is limited - you can use it to either (a) read/write CP/M disks written by other systems using the basic 8" SSSD format or (b) read/write MSDOS format 5.25" and 3.5" disks on systems running one of the x86 CPU boards.
As you will have noticed, all these modern S100 systems have been designed to use a CF or SD card for mass storage. If it is necessary to transfer files between a "modern" S100 systems and a PC, most either (a) use a serial file transfer software utility or (b) copy the files directly to/from the CF card disk image on a PC.
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Incidentally.... there is a discussion currently running in the S100 Computers Google Group on the topic of the S100 ATX motherboard I mentioned above. Someone has posted photos showing their recent build using the S100 ATX motherboard I mentioned previously, installed in a modern (and very inexpensive) Corsair-brand ATX PC enclosure.