Couple of things, not arguing that the 1650-1 made more power than the Allison, it did because it had a larger diameter impeller (supercharger). That is a fact.
Indeed, the bigger impeller was one of key ingredients of Merlin's power. ANother is that compression ratio was low, some 10% lower than on the V-1710, and 10-25% lower than on the DB-601/605 - that meant the Merlin took overboosting very well, more boost = more power in linear fashion. On 100 oct fuel Merlin III was factory aprooved by factory to make up to +12 psi boost (54 in Hg, around 1.9 ata) by 1939, with some subsequent types quickly going to +18 psi (67 in Hg, ) by early 1942. By time 130 grade fuel was available (~mid 1942?), better Merlins went to + 21 psi (~73 in Hg).
But the two figures listed in the "Engine Ratings" column (below the Takeoff rating) are for low gear (1240hp/3000rpm/11500') and high gear (1120hp/3000rpm/18500'). Takeoff was in low gear (to not overboost the engine at low altitude where the air is thicker) and then manually shifted to high gear at 11500' with critical altitude being 18500' to draw in more of the thinner air at higher altitudes.
And the single speed Allison was in no way a disadvantage. Later models (starting with the 1325hp V-1710-63) were equipped with an automatic boost control or automatic manifold pressure regulator (same thing). The maximum boost (or manifold pressure) for the engine was preset and this gizmo mounted on the carburetor limited boost to at or below that preset amount. In other words you couldn't blow up (overboost) the engine at ANY throttle setting. This eliminated the need for two speeds, manual shifting or automatic shifting. And this device apparently worked very well and was very dependable since it was used on most all the engines Allison manufactured thereafter.
So, with no throttle management the pilot could set the boost control, firewall the throttle and not overboost the engine at any altitude. This eliminated a lot of pilot workload.
I'm not sure how you can say at face value that 1-speed V-1710 was not in disadvantage vs. 2-speed engine, particulary vs. V-1650-1.
Later models of V-1710 are exactly that - later models. They lagged behind the V-1650-1 by 8-10 months, meaning that engines powering the P-40s and P-39s in 1942 were making 20% less power at altitude than V-1650-1. I will say that having less power = being in disadvantage.
Automatic manifold pressure regulators were not endemic to the V-1710.
Back to the two speed supercharger, the disadvantage was that in low gear power started to decline almost right away as the plane gained altitude and the air began to get thinner, so by the time you reached the shift point (11500') power was lower. Then you shifted into high and power steadily increased up to the critical altitude (18500') when it began to fall off again (just like low gear). This resulted in a sawtooth performance curve for both the engine and airplane. The Allison didn't have that problem (especially with the auto boost control) as it made 1325HP at takeoff and maintained that figure up to 8000' where it began to decline due to the thinner air.
Please, take a look at the tables. At 11500 ft, the V-1650-1 makes 1240 HP, vs. V1710-39 making 1160-1170 there. Or, at 11800-12000 ft, the difference is some 70-80 HP, while above 15000 ft we have the V-1650-1 making 25% more power. Sawtooth or not, nowhere where mattered the V-1710-39 and similar were not matching the power of V-1650-1. The V-1650-1 was making 1325 HP up to 9000 ft. And again at ~15000 ft due to having another S/C speed and a sizable S/C, despite the thinner air.
The Merlin 20 series from 1943 on were good for 1600 HP for take off, vs. 1200 HP on the 1-stage V-1710s from same time.
take a look
Only real problem with the Allison was that the Army insisted on designing planes around it that just weighed too darn much. The P-39 weighed around 7650#, the P-40 weighed 8400# and the P-51A weighed about that also. 8400# divided by 1150HP is 7.3 pounds/HP. The Me109G6 weighed 6800# with a 1475HP engine or 4.6 pounds/HP. You can see the problem.
Granted, the US fighters were over weight. However, Allison have had lagging too much with introduction of more powerful engines when compared with RR and DB, they managed by late 1942 to equal altitude performance of the Merlin III from 1937. Let's recall that every important US engine in 1944 was with 2-, 3- or variable-speed drive, unless a turbocharger was involved.
BTW - the P-51A have had 1480 HP max, the Bf 109G6 around 1550 PS (fully rated) or 1400 PS (restricted from mid-1942 to Oct 1943). Sure enough, the G6 have had better altitude power.