Wouldnt it make more sense for the system without the disk drive to have more storage?
Thats supposed to be the "budget" system. The one coming in at $399.
Companies do that all the time. The budget system will have the lowest margins for them' they may make only like $5-$10 off each unit sold. Then the premium system, the one that has more bells and whistles, will give them much higher margins. Unknown to the consumer the benefit of having twice the storage and a disc drive won't cost them more than an extra $40 on top the base console. But they get to charge them $100 for it.
Having a stand alone external disc drive that costs like $79 or something lends to the "added value" impression of the more expensive SKU.