I can see how the EE is thinking on this issue. Since the IG Conductor is used on the Dedicated IG circuits, the largest OCPD value would be 20 amps [unless there are circuits of higher amperage...???], so even with a #6 cu it would be "Overkill" in a way.
Minimum NEC requirements would be the angle the EE is using when addressing only one IG bond for Parallel Feeders.
The minimum will allow only one IG bond run from the panel to the source.
It would be different if this was the EGC, but still it wouldn't hurt to include a #6 with both Feeder sets.
I believe the system that Nick is describing would be an SDS [Separately Derived System].
The Transformer mentioned would be an Isolation type Step-Down Transformer - Like 480 VAC 3 phase Delta Primary x 208Y/120 3 phase 4 wire Wye Secondary.
In this case the proper point to land the IG conductor would be at the X0 Ground bonding point [where the EGCs and the GEC bond to the X0 termination].
The use of a #6 cu is a very common spec for IG bonds. I typically spec that size. It's larger than needed, but that's a good thing!
Back to Nick,
If the Subfeeds aren't really long, would it be easy enough to simply include a #6 IG bond in both Subfeed conduits?
This would satisfy everyone - you will not have the 250-122 item bugging you [it will be installed to your satisfaction], and you will not need to resolve EE / EC issues, nor wait around for RFIs to be answered and all that baloney!