I'm just updating this thread with some closing remarks in case it helps others.
Basically there are two features which would be interesting to allow independent management of the units when running FGCP a-p mode.
#1: ha-reserved-management/ha-direct/ha-mgmt-interfaces. There are too many touchpoints and workarounds with this approach and they're not well documented. I had to fix local-in, then FMG and after all that I couldn't get outgoing DNS requests to work.
#2: Use a standalone-management vdom as documented here:
Option #2 is definitely the way to go, although you lose 1x of your VDOM licenses. It's completely broken in 6.0.x code though and I ran out of time to test this in the newer versions.