Marjus Dettweiller in Switzerland reports that with the availability of FX CAST, a cycle accurate 68000 CPU and cycle accurate chipset for the FPGA based MISTer system (information and download at http://atari-forum.com/viewtopic.php?f=28&t=34554 – emulates Atari ST/STFM only, no STE functionality and no blitter), it is now known that the Atari version of SMSQ/E works on it. DD disk read/write is via .MSA disk image.
Get FX68K from https://github.com/ijor/fx68k The Atari version of SMSQ/E is available to download from Wolfgang Lenerz’s website at http://www.wlenerz.com/smsqe/