Antenna questions.

Mrh,
My suggestion would be to try out the company's setup, at least for a reference, unless it's one of the Cascadias or Volvos or others that use multiplexors and lots of jumpers to run a handful of devices off of just two antennas. It might turn out that (for once) someone did a decent job of running the CB mount and coax in this one for you. Worth a shot, anyway. And SWR is related to frequency, not individual radios, so if it's good with their radio, it'll be good with any.
If it turns out to be the traditional suckage, though, there's nothing to be lost by running your own coax and mount. The only thing I'd do, however, is when you go to take the truck out on a run, remove "their" antenna from their mount, and put your antenna on your mount. There's really no potential for interference by the mere presence of another mount and coax nearby to yours, but having another whip standing up next to yours a few inches away will almost certainly detune yours, changing the impedance and radiation pattern every time the whips change position relative to one another.
If the design of the company's antenna is such that it won't come loose from the mount, you've got two choices that I can envision: either loosen it and pivot it so that it points downward (looks goofy, but you can tell other drivers it's your Super WhizBang 9000 Mobile Delta Beam or sumpin'); or mount your antenna, coax, and mount on the opposite side of the truck. In that case, hopefully, the company put theirs on the passenger side, so tree branches & stuff will kill theirs instead of yours
But no, with the exception of the antenna itself, the existing installation won't interfere with what you intend to put in yourself. But I'd give theirs a try, just in case they did it right to start with; you might save yourself $50 worth of parts.
73,
Handlebar