An Allison in a P-38J could maintain sea level power to at least 26K feet. And about 90% to 95% all the way to about 30K feet. No Merlin in any P-51, at least in factory tune, could maintain sea level power that high. The Merlin in the P-51D was good below 18K, and then again around 22K, right after the supercharger gear drive shifts to the high speed gearing. Some tables say the Merlin in the P-51D was down to around 1250 or so at 26K, and down to 900 or so by 29K.
We were not discussing Merlins in Spitfires or Mosquitos, we were discussing P-51s. Yes, there were Merlins tuned specifically for high altitudes. They had different supercharger gearing. Those engines could not operate at peak output any where other than those high altitudes, or they'd overboost and blow up.
The limitation on ANY crank driven supercharger, especially in aircraft, is that the supercharger must be both sized AND geared for a specific output at a specific altitude. To a limited extent, this can be overcome with a two speed gear box, as the Merlin had. However, you still have only two narrow peak operating ranges, and performance suffers outside those operating ranges. With the Merlin, you have two ranges of about 5K or so where it has good efficiency. Where those two ranges are depends on the supercharger gearing. Further, you can only spin a supercharger to a certain speed, beyond that point, efficiency drops dramatically, and it begins to absorb a much higher percentage of the power it adds.
A turbocharger will also over speed, there were warning lights and buzzers on both the P-38 and the P-47. Usualy, around 30K or so, the GE B series turbocharger on the P-38 and the P-47 could no longer maintain full pressure without exceeding the RPM limit. However, the turbocharger has a far wider operating range than a supercharger, and it also has far less parasitic drag, since it uses exhaust pressure and heat to power it, as opposed to directly robbing HP at the crankshaft as a crank driven supercharger does.
Yes, if you added a turbocharger to the Merlin in the P-51, the exhaust would change drastically. The only place to mount a turbocharger on the P-51D would be behind the fuel tank in the fuselage. That would mean the exhaust would go back there, under the cockpit, over the radiator, to the turbocharger, and then exhaust there. The pressurized air would then have to be ducted forward, through an intercooler, then into the supercharger intake. You'd also have to run oil from the engine to the turbocharger and back. I do not think the Merlin could deal with it, the burden on the oil system would likely be fatal, as the oil system is marginal at best. I doubt the cooling system would handle it either.