BlackOps Unleashed made it so the T2 & T3 factories could be produced by the respective tiered builders (T2&3 engineers, ACU with T2&3 engineering modules & SACU).
The FAF version (v10) does not allow that. In FAF the vanilla_FA factories became the HQs, they are basically the same thing (with minor differences).
I request that this feature be added (back) into the mod, since it was originally in it. Or at least make it some kind of setting option so those for or against it could choose whether they want to allow it in their match or not.