I am thinking about an add-on SCSI interface, either software driven through the FPGA or using a real 53C80. Everything for the Mac is SCSI based for external peripherals, so having SCSI is not an option for Mac emulation.
If you have a particular SCSI device you want to connect to it then you need SCSI connector (or at least a SCSI to USB/SATA/whatever converter), but whether that is for a mac emulator or you want to emulate an A1200 and hook it up as an IDE drive should be irrelevant. If the FPGA replay supported ATA/SATA then there should be no problem making devices connected to it appear to the emulated mac as a SCSI peripheral connected to a 53C80.
You shouldn't need a different expansion board and set of peripherals just because you want to emulate a mac or amiga or st etc. The idea is you can emulate a mac one minute and a cd32 the next, if you want to use real CD's on either then you shouldn't have to plug a different drive in. It would be terrible if trying to emulate an ST with an external drive required a new external board and an ACSI drive.
The majority of course will want to just emulate without any real peripherals and have them all virtualised from images on their SD card anyway, CD drives are likely to be the only real device most people would want to use. The majority would want to use a hard drive to store more images, not actually use the hard drive direct (although both options should be allowed).
The HDMI mode that allow HDMI+audio uses a different line coding. So the existing HDMI encoder chip on the FPGA Arcade can't be configured to enable audio.
That is a shame, those ATI DVI->HDMI converters would be a cheap way around the licensing issue if the hardware shipped as DVI but could be upgraded to generate DVI+audio later on by some unscrupulous individual.