How do U.S. research institutions typically reimburse a faculty candidate's airfare costs for multi-city trips?
When looking for a postdoc and visiting multiple labs, I was asked to split the reimbursement for travel costs between the institutions. The exact details of how to split were left to me.

Most institutions expect to fund the entire trip for faculty candidates, so I don't foresee any problems with you asking them to pay less than what they expected.