Hyperion support contacted me and they were able to use the UAE config I provided to determine the issue was, in fact, related to mmu.library. OS 3.2.x ships with MMULib and is setup to load mmu.library via SetPatch. Per recommendation, I contacted the MMULib author. Thomas was very responsive and helpful. (The Amiga community is the best!) He was able to determine the cause of the issue (via emulation) and provided a solution. Essentially, the GVP 1230 Turbo+ II is using an undocumented memory location that needed to be mapped by mmu.library.
If you have a GVP A1230 68030 w/MMU and A1291 SCSI Expansion, adding the following line in envarc:MMU-Configuration will allow the controller to behave properly:
; For GVP A1230/A1291
For 2017 11 SetCacheMode 0x03000000 0x0400 Valid IoSpace CacheInhibit
Thomas is looking into a change to GVPInit to integrate this configuration, but the above config will fix the issue for now. Lastly, I was able to reproduce the issue on OS 3.9 after installing MMULib. As soon as mmu.library loaded via patched SetPatch or MuTools SCSI devices no longer worked. The same MMU-Configuration addition works on OS 3.9. My external ZuluSCSI is now working great on the A1291.
-Jeremy