When setting up a mission with an Independent force as the primary opposition, it would appear that their objective status (and/or units) are completely ignored by attacking forces. Is this the expected behaviour?

In the test mission I threw together; BLU (Invasion) vs IND (Occupation) resulted in objectives in BLU's TAOR are Reserved, with Reserve orders issued to every objective in IND's TAOR. No attack or defend orders are ever given by BLU's OPCOM. Left to their own devices, BLU's OPCOM will issue no other orders beyond this initial set-up phase and objectives within IND's TAOR will slowly become unassigned as BLU units are sent piecemeal to capture "unoccupied" objectives. IND's OPCOM on the other hand, issues orders normally at all times.

The above appears to be true in all possible scenarios vs an IND OPCOM. BLU/OPF OPCOMs never seem aware of IND units, though they will fight one another as determined by IND's hostility settings.

did you sync the ai commander to the mil/civ/cust. objectives?

Yes.

As I said, this isn't an issue of them not seeing objectives, which would be the case if commanders weren't synced to objectives. This is how IND_F interprets the mission above.

And this is OPF_F...

The same mission with IND_F replaced by BLU_F...

As you can see, when OPF_F is fighting IND_F they issue no attack or defend orders. They attempt to reserve enemy occupied objectives regardless of IND_F presence and only issue a handful of commands to their initial forces. Compare this to their behaviour vs BLU_F, where they attack and defend objectives as one might expect.

I was more looking for clarification of whether this is supposed to happen or not as I'm yet to find a situation where a Red/Blue Commander acknowledges the presence of a Green Commander, leading me to believe it is either intentional or broken.

Yes. I did wonder if that might be the cause, so I've tried with them set hostile to one faction and hostile to both. The result is always the same. They engage one another if they meet in the field when set hostile, but the objectives remain as pictured above.

Sure.

Here it is.

CBA and Alive loaded. Just a basic template to test out the variables that were causing my issue, but the problem is immediately obvious when viewed from the OPF_F perspective.

Looking good so far!