The nipple sticking up out of the carb is the stock Q-Jet bowl vent that was used only by Pontiac on all 1971+ Q-Jets. Since nobody is going to make an aftermarket air cleaner base specifically for 1971-1979 Pontiac Q-Jets, the answer is, yes, you drill a hole in your aftermarket base to make it fit. No problem. The other alternative, as stated above, is to use your stock air cleaner base with the aftermarket filter and filter top.
The other thing you're going to have to do with an open-element aftermarket air filter is to get a valve cover breather for the passenger side valve cover - there won't be any way to use the stock breather tube that goes up to the side of the stock air cleaner housing. You have to have some breathing capability on that valve cover to keep the PCV system correctly operational.