Yes, that is the difference--ported vacuum on the manual trans carbs and manifold vacuum on the auto trans cars. Seems like there is one other minor difference too, but I can't remember off the top of my head. The auto carbs will work fine on a manual trans car.
In fact, if you have a big camshaft in the engine, you will have to hook the vacuum advance to manifold vacuum to get it to run right, otherwise it will stumble and fall on its face when you let the clutch out and the engine rpm drops a little, causing the vacuum advance to retract and it is downhill from there. On an engine with a stock camshaft, the ported vacuum on the correct man. trans carb works fine.
I think the reason they did the man. trans carbs different like that was to meet some basic emissions requirements that started in 64. More retarded timing at idle (as a result of ported vacuum), helps reduce NOx and CO. It is more of a problem on manual trans cars because there is zero load on the engine when idling in neutral. Auto cars are always turning the torque converter and pump in the transmission.
And if you ever find a correct rear 2-4's, manual trans carb, let me know and I will buy it from you for some good $$ I have never even seen one personally.