You might need to cut three corners. But if the three options, I would favor milling off the hump. Besides, bare compound slides are generally cheaper than decent quality QCTP's. And if you do a decent job of modifying the compound, it won't affect the value should the time ever come that you (or your heirs) need to sell the set.
On the subject of milling the hump, if you have an Atlas Milling Attachment, the compound slide and swivel will mount on it in place of the vise. Just don't make the mistake of trying to use the swivel as a rotary table.