They’re not actually saying MS charges 50% commission. They’re saying taking everything into account, including the reduced pricing structure, they receive 50% less than sales direct through PayPal.
Personally though I would think they’d probably sell an awful lot more through the market place so it should even itself out or proove to be even better in the long run.
They should also think themselves lucky to be able to tap into the market place… I put an application in about 5 months ago and it’s still under review!