What reasons? I just thought the issue had to do with specialized high altitude fighters.
I'm not sure what the projected service ceiling, critical altitude, and combat altitude the XP-54 was expected to fly at, but in practice they had a critical altitude of around 28,500 feet. This isn't much different than the P-51. The P-51's seemed to be able to routinely operate at 31000 feet during combat operations over Europe. I'm not sure how high they flew for B-29 escort.
The problems I can see with the guns are temperature related, as for the radios and instruments, I'm surprised altitude would have much effect. As for engine ignition systems, why would that cause a problem?
One group, squadron, flight, or whatever, of fighters didn't escort the bombers the entire distance, they did it in relays.
Each fighter group would have only been at that high altitude for the part of the mission that were doing the actual escorting, not before the rendezvous with the bombers, and not after they'd turned over the escort duties to another group.