Alright call me crazy, stubborn or persistent, but I just couldn't let this go. I barely slept last night thinking about different ways to get the GoldenGate working and today I ended up trying the following:
Pulled out one of my older A2000's which was pretty much a blank canvas. Just the case, motherboard, PSU and the GVP3001 accelerator. It has 8Mb of Z2 RAM so jumpered that to 4Mb. Then added a 4Mb SupraRAM jumpered to 2Mb which gave me a total of 6Mb Z2 RAM.
Then I added a Matze "IDE-LAN-Clockport" card for IDE hard drive, except I used a basic compact flash IDE adapter and a Sandisk 2Gb card.
Next up the GoldeGate to a free bridgeboard slot and then the hardware side of things was done. Now to a fresh install of Workbench, which was quick and easy using WinUAE and ADF disks.
So the changes I've made so far are:
A2000 motherboard rev6 --> rev4.1
Kickstart 3.2 --> 3.1
OS3.2 --> 3.1 (clean install)
DH0 file system, PFS --> FFS
Added the adapter between the 68k CPU and the motherboard socket
I then proceeded installing the patched GoldenGate library and drivers and on with the testing! "CPU nocache" in the shell and of we go, or so at least I was hoping.

But alas, no dice... "error 51", can't find yadda yadda gate.
Now this is where the crazy and stubborn part comes in: I kept at it and as a last effort I thought about using the original GoldenGate library. Replaced the patched one with the original one, turned off the caches and:
IT WORKED! 
The GoldenGate buzzed and booted very nicely up to the bios. Now I've never even gotten to the settings page (by pressing S) before, but now I do! Consistently! I kept rebooting the Amiga and starting digger thinking this was just a fluke but no, the damn thing seems to work with this setup. Digger even starts without disabling the caches, it does it automatically!
I'm not sure what change made the difference but this opens a whole new world for me. So many ISA cards to test, DOS games to try and so on.
One last question for you experts though: can the empty "option rom" slot on the GG card be used in any way? I was immediately thinking if it was possible to put an XT-IDE boot rom in it?