Was there any intrinsic design feature that precluded Allison engines from powering single engine fighters over Germany at 25000 feet, of was it all just a case of the American engine being hobbled by the thinking of the time - that high altitude fighters weren't required?
This is often repeated but has little basis.
The US wanted high altitude fighters, they were required. The USAAC had turbo P-30s, turbo Airacuda's. 13 YP-37s, the P-38 and P-39 prototypes. A turbo P-35 and a P-35 with a two stage supercharger plus a P-36/Hawk 75 with two stage supercharger were at the 1939 fighter trials that led to the P-40 order.
The 1st problem was that NONE of the high altitude planes were really ready for SERVICE squadron use.
The 2nd problem was that Allison was a very small company when it got the order for the engines to power the 500+ P-40s in the April 1939 order. Plant expansion and tooling up to make engines on a production line basis instead of tool room batches of a few engines per month meant that R&D on the high Altitude versions got put on the back burner (if not back in the refrigerator) until the production thing got sorted out. Production got even more complicated when Allison got permission to export the engine to France and Britain which meant an even higher production volume.
3rd problem was that Allison had spent a bunch of time on other Army requirements like the P-39 remote propeller, the Airacuda remote pusher engine set up, the P-38 handed engine and the V-3420 double engine.
GE was supposed to be handling the turbo for the high altitude planes.
Army was handling the turbo controller?
There is a recipe for success (not).
other factors that hurt US fighter high altitude performance in the early part of the war were, 1. US fighters carried more fuel than
most other counties fighters. Given similar field requirements (landing and take-off) this means a bigger airplane, in general. 2. the US slapped a heavier armament into it's early aircraft (I am not saying better, I am saying heavier). 3. The US had a higher "G" limit than some other countries (not all) so the structural weight was higher. It adds up to planes that were hundreds of pounds heavier than their British or German equivalents in the early part of the war. Given roughly equivalent engines the US planes struggled at higher altitudes.
Until Hooker came along the Merlin wasn't that much better at high altitudes. Once he showed up
everybody else was trying to play catch-up.
Try slapping a Merlin III into a P-40C and see what kind of performance you get?