Military multiengine fighter time doesn't "count" as centerline thrust -- that's the mistake in your thinking. The centerline thrust only refers to a restriction placed the Commercial tickets issued to military-only trained pilots who take the FAA competency test.

If you have your multi BEFORE the AF, you won't have a centerline thrust restriction, obviously. If you are a military-only trained pilot, then your Commercial will have the restriction until you go do a Vmc demo with an FAA examiner and get it removed.

There's nothing magically different about the multiengine time you get in a military fighter...it's not "centerline thrust multiengine" time. The restriction is on the ticket of the military-trained pilots, not on the airplane. The hours still go in the multi column of the logbook and still count juyst like any other multi hours at the airline interview.