I would like to note that the SR-71 normally flew at 80,000 feet.
At about 63,000 feet, water boils at body temperature. Beyond this altitude, bottled oxygen is useless; mammalian, avian, or pegasus lungs simply do not function. RD wouldn't survive without a pressure suit.
Admittedly, if her lungs etc. could withstand breathing air at higher pressure than her surroundings (which would kill a human), she might be able to get away with just an oxygen mask.
Also, at such high altitudes jet engines work (not very well though), because a significant part of their reaction mass comes from the fuel burned. RD's wings, however, can only generate thrust by pushing the ambient air backwards, which doesn't work too well when she's only displacing 3% as much air per wingbeat as she would at sea level. This would most likely overpower the drag reduction from the thinner air.