I'll have to look for some of my old technical books, but, until I find them I'll try one more crack "un-aided". Take a small straw and pull air through it. You won't get much air but there will not be much resistance to flow (similar to a partially closed throttle with little to no restriction). If you take the same straw and put a piece of paper over the end and draw through it again (partially closed throttle but with a restricted air filter). You will get less air through it in a given amount of time or it will take a lot more effort to get the same air flow as before without the restriction. If you do the same exercises with a really big straw, simulating WOT, the same will happen. Yes the throttle blade limits the volume of air for a given amount of time thus controlling the RPM but a restricted air filter will cause the engine to work harder because the pressure differential between the area before the throttle blade and the area after the throttle blade will not be as great.
Think of extremes. For example, no air filter. The area before the throttle blade is basically atmospheric pressure, the area after the throttle blade is less than atmospheric because of the pistons moving down in the cylinder(s) with the intake valves open. The atmospheric pressure is pushing into the engine because of the pressure differential. At low throttle positions there is a great differential, i.e. there is a lot of "vacuum" in the intake manifold. At WOT, there is a little bit of "vacuum", but its still there and the throttle blade is wide open with the least amount of resistance.
Now imagine a very clogged air filter. The pistons are still going down and creating a low pressure area. Air is being drawn in but there is less air available because the air filter cannot supply as much air as the engine would like. The area before the throttle body is no longer "pressurized" as much as atmospheric pressure. The engine will compensate somewhat because vacuum should go up in the intake manifold so the pressure differential should still exist. However, now the engine is operating at increased vacuum in the intake manifold. Normally, high vacuum is desirable for fuel mileage because the engine will draw the air or air-fuel mixture in more efficiently (remember those old MPG gauges that were nothing more than a vacuum gauge?). However, that is when the air filter is not restricted. When it is restricted, high vacuum is a side-effect of that restriction and is not creating any efficiency. When there is very high vacuum in the intake manifold non-beneficial things happen. For example, seals can be damaged, oil can be drawn into the cylinders past the rings or the valves or the seals, and the engine has to work harder to overcome the low-pressure (aka: vacuum). Imagine a jelly bean in that big straw from earlier. Put the bean in the middle of the straw, now suck on one end of the straw (low-pressure) the bean wants to move towards the low pressure, not away.
Now, the way I just explained it is not exactly accurate but was an effort to explain it better. In reality, there are three pressure zones: before the throttle blade, after the throttle blade, and in the cylinder. Inside the cylinder on the intake stroke is where the lowest pressure is. So the piston its not directly working AGAINST the low pressure of the intake manifold but rather it is getting less help when the filter is clogged because the pressure differential between the cylinder and the intake is smaller. The more pressure differential, the better.
I hope this made sense as I've had a couple beers tonight.
I also hope I fully understood your question.