Exiting Belize Citizens and Permanent Residents of Belize don't pay anything. Visitors/tourists (and I think QPR) pay BZ$37.50 (US$18.75) payable in BZ$ or US$ at the land border. Departing Ambergris by water taxi to Chetumal might be cheaper -- in this case, I think only the BZ$7.50 PACT fee is payable. Or is it... only the BZ$30 departure fee is payable and not the PACT fee?
Entering Mexico from Belize Visitors to Mexico receive an FMM (visitor's card/form/visa/whatever) at the border. If you stay in Mexico for 7 days or less AND return to Belize, there is no fee to pay. If you stay in Mexico for 8 days or more, the fee for the FMM is MX$262. The fee is not paid at the border but at a bank before you depart Mexico.
Departing Mexico (to Belize) Hand in the FMM form. There are no departure fees. Beware of the scam where the Mexican officials ask for money upon departure.
Both CC and SP are islands. Most likely the cost difference relates to what is being built in either place. The houses tend to be much more modest in CC than SP. Just a guess, probably a few more reasons I can't think of.