I’m pretty sure it does take the large thermostat. A friend had one of those ‘65-‘66 2-4 bbl Medium Riser intakes without the engineering numbers, and I thought I might have a picture, but haven’t found it yet. But Ford didn’t even have a FE thermostat housing for the small thermostat yet in ‘65, that didn’t start getting phased in until during the ‘67 model year.
I think it’s probably the same for both, but there was also ‘65 427 Low Riser 2-4 bbl intake manifold, so you may want to specify which one if you think it matters.