No the B-29 could fly higher than all the other major bombers including the Lancaster, B-17, and B-24. Besides the Pressurized Cockpit was really fricken nice at those altitudes.
Service Cielings
Lancaster: 23,500 ft (8,160 m)
B-17: 35,600 ft (10,850 m)
B-24: 28,000 ft (8,500 m)
B-29: 36,000 ft. (10,973 m)
However for the most part over the ETO that would not have mattered because the Luftwaffe had aircraft that could flyer higher than that. So in that case you are correct in saying that the Japanese did not really have a true high alltitude fighter to deal with the B-29.