"Your post about use of capital assets on an individual contract being dispositive regarding the allowability of FCCOM with respect to that contract is just wrong. "
I was merely making the shorthand point illustrated by your scenario above: maybe the CO was saying that Engineering labor was not an appropriate direct charge for the effort in question. I've seen stuff like this when a contractor proposes engineering work on a follow-on production contract (i.e., the instant contract is not reasonably expected to employ the engineering DC & O/H pool to which the allowable FCCOM is applied).
If I as CO don't accept the direct charge and its O/H pool as reasonable, allowable, and allocable to my contract, I certainly don't incorporate the associated FCCOM into my counter, regardless of CAS. That is a possible circumstance in which FCCOM would not be "allowed", as the OP stated. (I suspect the OP was a bit imprecise in their terminology when stating the CO said FCCOM was "not allowable", which cannot literally be true).
You almost make it sound as if the mere fact that the contractor proposes FCCOM makes it acceptable - that's not what you meant, is it?