In the 9 cruises I've done with Regent so far, I have not had an upcharge. I do the deviation at 210 days out ($175) and also fly from a non-gateway city ($250), but those are the only charges I pay. I think you have 3 days to accept their proposed route, or ask for a change.
Also, you can have them book your flight arrival up to 30 days before embarkation, and return up to 30 days after debarkation. Can even use other airports (debarked in Barcelona, flew home from Lisbon 3 weeks later).