Yep. Mine flashes. Several times. Maybe 4 or 5. I was behind a newer ST today and it did the same. By the time I realized it, I did not catch the count.I never noticed the Focus's third brake light flashing. Then again, I don't usually look at my own brake lights when panic braking. I believe all the Mk3s have LED third brake lights, at least all hatchbacks do. My 2013 does.
Appears as though you are correct. Looks like it is LED either way.