I also had to question why Swissport would do the handling at KEWR where UAL is the biggest airline. It's been several years since I was ramp guy, but I never saw Swissport working a flight at EWR.
My solution was fairly simple: Edit Swissport and UAL in the configs for each vehicle.
The only thing I have to be aware of now is after the Standalone Addon Manager update, the baggage tractor config always reverts while the other vehicles do not.