What NGD said. OPSPEC = yes.
Government contract, super-secret squirrel TLA ops, without a 135/121 cert and OPSPEC = no it does not legally count.
An OPSPEC is an extension of the FAR's so any requirement therein is regulatory. Internal policy from other government agencies dose not rise to the level of federal regulation.
Now I have seen guys doing TLA ops who could not log their flight time in their personal book because of classification issues. In that case the employer would usually provide a formal letter at the end of their service detailing the type, amount, and time frame of the hours logged without getting into sensitive specifics like exact dates and locations. They might not even divulge the exact aircraft type, but might use general terms. If said employer is willing to give you a letter detailing SIC time, that would work for me. Given the nature of those missions I personally would have no trouble accepting that as flight time, with a letter in hand.