Ju 86R2 managed to get to 50,000ft, presumably with GM-1. The August 28 Spitfire IX intercept seems to have reached over 44,000ft. The Ju 86 was at about 42,000ft when it reacted to the Spitfire and responded by jettisoning their bomb, engaged the GM-1 and began to climb. It's possible that had the Ju 86 begun evasive measures earlier they may still have gone beyond the Spitfires altitude.
Germany's U-2 - WW2s Highest Air Combat - YouTube
The BMW 801TJ-1 was flown on the Ju 388 and Ju 88S2 since 1944 and understood. The Germans had valuable high altitude test chambers wind tunnels that could simulate any temperature, air pressure and air speed to assist in engine development. This greatly helped German axial jet engine development.
You seem to fear the BMW 801 TJ wasn't systematically developed by engineers who knew how to do thermodynamic calculations or without the ability to manage a systematic development and test program.
The BMW 801TJ-1 had some issues with excessive fuel consumption not altitude performance. The BMW 801TJ-2 was already test flying and the BMW 801TQ was soon to follow, all with improved turbo superchargers etc.
The Luftwaffe's high altitude program was more focused on ultra high altitudes to escape interception than the US one which was focused in high speed cruising to high altitudes.
The Ju 488 V401 bomb load is unclear to me. Some sources say 3000kg some say 2000kg. The aircraft inherited its bomb panier from the Ju 388K which was 2000kg but its possible it was longer given the Ju 488 was a fuselage stretch of the Ju 388. The much larger Ju 488 V403 had a wider longer panier and was rated to 5000kg (11000lbs).
Incidentally at the end of the video Mark Felton states that a spitfire V shot down a Ju 86 over the Mediterranean. This never happened and has been debunked. It's technically impossible for a Spit V to reach a Ju 86P however one Ju 86 did crash over 150 miles away the next day due to engine failure