As the Amiga sampling frequency may vary significantly but the output will not. A constant difference in frequency of course add another frequency, then there's aliasing etc.
I don't believe the Amiga sample rate does vary, all samples appear to be output relative to the colour clock.
http://blog.kebby.org/?p=11 http://eab.abime.net/coders-general/63227-low-level-workings-paula.html 3.58mhz is a little high to be outputting though. The Amiga will put that through some form of filter, even when the low pass filter is off.
From what I can tell the 2 bytes in the AUDxDAT register get output alternatively for 64 clocks, the audio changes when another 2 samples are loaded (either via dma or cpu). Which kinda sounds like it would cause a lot of noise artifacting, but apparently not (although paula does sound a bit crunchy at times).
You could do a SCSI-II controller in the FPGA (plenty of gates left), but I happen to have about 2000 53C80 chips sitting here to give me SCSI. SCSI is exclusively used by the Mac, and for the Mac emulation I will need SCSI support to access things like Syquest drives, CD-ROM drives, tape drives, etc.. all of the same stuff that is plugged into my A3000.
I would hope the Mac emulation will work without any real SCSI peripherals though, at that point you probably don't want to use a real 53C80 as you'd be limited to only having real peripherals or only having emulated ones. If you emulate the 53C80 then you can have a mixture of real and virtual peripherals, plus it would be nice if you could use the same interface for emulating any machine with SCSI whatever controller chip it uses.
Of course you can go ahead and make your own expansion board with a 53C80 if you like, but it is likely it will have a very small audience as everyone is likely to want the board with the real 68060 and the people who need an emulated SCSI controller chip will have to effectively redo the same work. While if we could persuade mike to just throw on some SCSI/IDE connectors (or even space for them) then it would meet everyone's needs (except your manufactured need of finding somewhere to put these 53C80 chips).