Boofhead,
Some discussion of the function of the throttle and propeller are in order, first. You can consider your engine to operate in two ranges, so far as the throttle goes. Barometric (or the normally aspirated range), and a boosted range. At sea level, where normal standard pressure is 29.92 inches...anything at 29.92 and below is barometric (on a standard day), and anything above that is in the boosted range.
The throttle is often misunderstood. Operators mistakenly often think they're somehow pushing more air and fuel into the engine by increasing throttle, when in fact they're doing somewhat the opposite. Think of your engine as a suction machine, or an air machine. You can compare it to a vacum cleaner. It sucks air in through the vacum hose, and blows it out through the exhuast. Your vacum hose is your aircraft induction.
You probably know that if you put your hand over a vacum cleaner hose, it makes a lot of noise, and the air pressure in the hose drops (as evidenced from the red ring on your hand, when you remove it). Because an engine is a suction machine, closing the throttle has the safe effect as putting your hand over a vacum cleaner hose; pressure drops. typically to about 13 inches or so at idle. Of course, even with the throttle closed, some air and fuel is still getting by the throttle plate...this is how the idle (and idle mixture) works.
If the throttle is opened in a normally aspirated engine, eventually you'll reach full barometric pressure...which again at sea level is 29.92 inches, and at five thousand feet is about 24-25 inches of manifold pressure. In fact, shut down the engine so it isn't "sucking" any more, and you'll read the barometric pressure on the manifold pressure gauge, where ever you are.
In a turbonormalized engine, the engine is capable of maintaining sea level manifold pressure (or slightly better, in many cases) up to the critical altitude (typically around 16,000 to 20,000')...then it starts dropping off. It does this by means of a turbocharger and wastegate system.
If you're operating the engine at less than the throttle setting necessary to maintain a boosted pressure (sea level barometric), then you're going to see manifold pressure drop off with a change in density altitude. Put into terms of your question, if you're operating the engine at 25" of manifold pressure, you're not using your turbocharger below 5,000'...you're operating in the strictly barometric range. If you climb, you'll see a change in manifold pressure unless you increase throttle and use the turbocharger to boost manifold pressure above barometric. This is normal.
That's the throttle. Nor for your propeller.
Your propeller will attempt to maintain a given RPM when it's in the "governing range." That is, the propeller governor has the ability to keep the propeller RPM constant, but not all the time. On the ground at idle, for example, the propeller blades are resting on their "low pitch stops", and the engine RPM isn't high enough to actuate the propeller...the propeller acts like a fixed pitch propeller. Once the engine is turning fast enough to enter the governing range, the propeller control may be used to reduce RPM, and the governor will maintain that RPM.
If you're maintaining 30 inches of manifold pressure and the propeller is holding 2500 RPM with the propeller control all the way forward, you can expect the engine to maintain 2,300 RPM once you retard the propeller control enough to achieve that setting. You can then climb and descend and the propeller RPM will hold that setting.
If you retard the manifold pressure enough, however, the propeller blades will no longer hold that setting. Once the throttle is reduced enough, there's not enough oomph or torque driving the propeller. Where ordinarily pushing up the throttle on a constant speed installation will cause an increase in blade angle to maintain the same RPM...pulling back the throttle will cause a decrease in propeller blade angle to maintain the same RPM. Eventually the blade angle will decrease enough that the propeller blades are resting on the low pitch stop...and can't decrease any more...and then the only thing that's going to happen is that the RPM will decrease. The propeller has run out of ability to maintain that airspeed, because it's reached it's mechanical limits.
If you're operating at low manifold pressure settings in cruise, you may be low enough that you can't maintain RPM (especially in a climb). The propeller reaches a point where the blade angle is limited by the low pitch stops, and can't decrease any more in an attempt to maintain RPM...then RPM simply decreases.
If you're operating at a low manifold pressure setting in cruise, and climb or fly from a cold area to a warm area or to an area of low pressure, then the manifold pressure will decrease, just like in a normally aspirated engine. In fact, the engine is acting as a normally aspirated engine because you've retarded the throttle far enough that you're not taking advantage of the turbocharger.
If your'e seeing higher than normal fuel flow, you're actually experiencing lower than normal fuel flow...because the fuel flow is measured as a pressure differential...a plugged injector makes for a leaner cylinder and hotter cylinder, but also shows as a higher fuel flow...something you might not see or recognize without a multi-point cylinder and exhaust temperature monitoring system.
On approach to landing, with low manifold pressures, you're going to see the propeller behaving as a fixed pitch propeller...again because the propeller blades are resting on the low pitch stops, and can't increase their angle any more. RPM will be a function of throttle setting, and airspeed. If throttle setting remains constant, then a higher airspeed will yield a higher RPM, and a slower airspeed, a lower RPM...because airspeed drives the propeller at low power settings.