Don't the locking skewers assemble together just like a QR? I don't know how these work, but if they don't have a c-clip at the ends to add that extra security??, I don't think it will be a big deal.
However, if you find yourself swapping a lot, I can see this getting annoying real quick. I have a CX bike and had two sets of wheelsets, one for trails and one for road/commuting. As easy as it sounds, it started to become annoying. If you have fenders.. even worse..
Maybe you should get the security locks and a new bike rack...one that doesn't require the removal of the front wheel.