Just trying to point out that you got the dynamics just a little off when you said fuel would fly out of the air inlet if the manifold were positively pressurized. That's simply not true. Fuel will flow from the area of higher pressure to the area of lower pressure. Period.
And I disagree that boosted (also a 'proper' term for systems that aren't naturally aspirated) systems are a horse of a different color from the dynamic you were describing. About the only difference between a boosted system and a non-boosted system is you're pushing the air into the cylinder with a bit more pressure differential -- so you get more flow, which means more air/fuel in the cylinder and hence more power. Naturally aspirated systems function almost exactly the same as boosted systems do - it's just that you only have the pressure of the atmosphere doing the pushing. It's simple pressure diffential that causes any fluid to flow from the higher pressure area to the lower pressure area.
When the piston moves down the cylinder you've got an increasing volume. Take a fixed amount of any gas - and expand the volume that it occupies, and the pressure has to drop. Since the pressure drops below atmospheric -- atmospheric pressure PUSHES air into the cylinder. All boost does is PUSH that gas, or air, into the cylinder with a greater pressure differential.
With a throttled opening, the throttle plate limits flow. And that's how pressures lower than atmospheric occur in the intake - the pistons drop in the cylinder with the intake valves open, but the throttle plate blocks the flow of air into the manifold - voila, a partial vacuum is created. Some times these are (mistakenly) referred to as vacuum(s) -- a vacuum is the absence of any air/gas in the volume in question. What occurs in the intake is simply a reduction of pressure -- creating the potential for air to flow from higher pressure (upstream of the throttle plate at atmospheric) to lower pressure (into the intake and cylinder).
As long as the absolute fuel pressure is greater than the absolute pressure in the port, fuel will flow into the space, and be drawn into the cylinder along with the air flow. You can get a bit of reversion -- flow of air out of the cylinder through the intake valve -- if you have the valve timing to cause it -- lots of overlap. The exhaust valve is closing while the piston is coming up and intake is opening. The pressures are such that the exiting exhaust can be at a higher pressure than the air in the port. When that happens the exhaust pressure can limit or even reverse the flow (briefly - very small fractions of a second at high rpm). That's what makes for lopey cams.
Forced induction or naturally aspirated - a vacuum leak (if vacuum is created in the boosted set up) is a vacuum leak. Of course, once under boost, you can't have a vacuum leak. Because there's no partial vacuum. Leakage from a pressurized intake tract simply reverses the direction of flow - from into the manifold to out of the manifold.
Vacuum pumps to power accessories have been around for ages. Diesels have had them for eons - diesels have no throttle and hence pressure in the intake tract stays close to atmospheric - no partial vacuum. And, of course, boosted diesels can run higher than atmospheric pressures in the intake tract.
