Did they use Mw50 during their "comparison tests"?
No, from memory they were restricted to military to preserve the engine. Pilot guidelines are very specific about its extremely conservative use anyway, only in level flight and at a high airspeed as an emergency measure to escape combat, the Americans quoted the Focke Wulf handbook about it. Use was prohibited at low airspeed BFM. MW50 and overboost in general doesn't reflect combat performance of an aircraft, it's largely superfluous, use it to enter a speed race not evaluate a fighter plane.
Were they familiar with german systems and tuning them ?
Yes, engineers examined the aircraft in detail, reported on its anciliaries and systems (such as the blower system and overboost guidelines), as well as compared their findings with captured FW pilot guidelines and workshop manuals.
The pilots had to work harder despite the presence of automatic engine controls?
Yes, part of the hassle was the ridiculously noisy and very hot cockpit, it was very wearisome. Controls were excellent but moving the aircraft around gave the impression it was quite heavy and it would slip a lot through manoeuvres. In general it was more about being an exhaustive aircraft to balance on the fine edge of high performance BFM and like the entire 190 family has a slight shade of inherent instability. Doras can't match the way an Anton can flip itself into a directional change, no other aircraft can, but it can still do a controlled stall not many others can match. They did remark it was surprisingly well equipped, mostly they congratulated the kommandogerät/aeromechanical-screw as revolutionary technology. It was. But a Mustang simply fatigues its pilot less overall, even Räll commented on this.
Did their report imply that a proper built dora could perform better ?
Yes but it was more about refinement and seviceability than figures. You might toss around something like a 7-15km/h speculative figure for qualitive finishing disadvantages.
Their expertise and eperience were better than Eric Browns ?
Yes, Eric Brown has never flown a D-9. He flew Götz's D-13. It was hand finished, has a prototype two stage motor and was given to a kommodore for service trialling. It is nothing like a typical wartime Dora.