Just a hunch, but I think you may be misunderstanding how the modules work... I know you'll be aware of most of this, but it's worth going to basics just to make sure you have a complete understanding. Sorry if it's too basic! Also, please do correct me if I'm wrong on any of this. This is just my understanding, but it seems to yield the results I'm after.
Where you physically place the military placement modules generally makes very little difference unless it's a custom objective. The only real difference it can make is placing a HQ near the module if the module is set to do that. Same goes for adding multiple overlapping Military Placement modules. Unlike the CQB and civilian population modules, they each identify the same things and layering won't make them more efficient or pick up any more objectives. Filters control that. The only reason to have multiple overlapping placement modules is to create different weightings of units (for instance, one for spawning armoured groups in only the large objectives, another for spawning infantry everywhere), or trying to spawn numbers that don't fit with the standard settings (i.e. 300 would take two Civ - 1 x 100 + 1 x 200).
The best way to see this in action is using each of the modules in debug mode. A civilian placement will identify set civilian locations as objectives within the specified TOAR that aren't blacklisted. If there is no defined TAOR, it will set all civilian locations as objectives across the whole map. Obviously, filtering will change the size of the civilian location that gets set as an objective but you get the idea. Same goes for military placement module. I imagine you probably already know this! But worth reiterating that it doesn't really matter where the module is physically placed.
Syncing the OPCOM tells the AI commander to attack the objectives identified by the placement module. If you set the module to "Place Units", then units will be placed at all the objectives identified by the placement module (providing there are enough units to do that) and OPCOM will try to use those units to hold the objectives, regardless of where that module has actually been placed on the map. You could even put it way off the map and it will still work pretty much identically. If it is "Objectives Only", then no units will be placed, but OPCOM will try to take those objectives using other available units, according to their priority.
Think of it this way. These modules essentially define what the OPCOM can "see". If there are no placement modules synced to an OPCOM, that OPCOM is essentially blind and won't try to take any objectives, no matter how many units it has at its disposal. The settings within the placement modules define how many objectives are "revealed" to OPCOM by the module. If there are no filters on the synced module, all objectives of whichever type (civilian or military) will be revealed to OPCOM, and OPCOM will prioritise those objectives based on their individual value, rather than the module location. Having multiple placement modules won't change this value either, or the amount of objectives revealed.
Thus, if the OPCOM is synced to a military placement module but not a civilian one, it will not "see" civilian objectives, and vice versa. Or if the OPCOM is synced to a filtered placement module, it will not "see" the smaller objectives and will totally ignore them, no matter what happens during the battle.
So think of these things less as placement modules, but more as objective generators for synced OPCOMs, with the ability to scatter units in and around those objectives. This way, you can get one OPCOM to see all the civilian objectives and only large military ones, while the opposing OPCOM sees all military objectives, but only large civilian ones. So both have safe havens effectively, which works well for asymmetric.
The reason your BLUFOR are attacking what seem like OPFOR objectives is probably because the Civ Placement module you've synced them to has identified the main urban area as an objective, even though it is on the edge of it, and that this overlaps with what the OPFOR Mil Civ Placement has identified as an objective. So both are attacking the same objective because of their overlapping Mil Civ Placement modules without knowing anything about the other side. Does that make any sense? You can test this using debug mode.
With FATA, I'd definitely agree with @AUTigerGrad and say use a military placement module for BLUFOR. In my mission, the BLUFOR military placement module TAOR is basically the areas blacklisted by the OPFOR military placement (which is used for random camps). Also bear in mind that the military placement modules will only identify the southernmost base (and a few of the other FOBs / military installations) if you set the military placement module to "No Filter".
Hope this was useful in some way!