Well first of all, it may not interfere with the trunking system controllers but it might very well interfere with the reception by other users. Even if the chance is kinda remote, if it were my system I wouldn't want anyone else on the frequencies, not knowing where they would be or how much they would be using them.
It's a legal liability.
As it is, the vendor is licensed to operate an LTR system and they are in control of the operation of that system.
If they go allowing simplex users, they have no control over how the simplex users operate. Or HOW LONG they operate. Or Where. The license is in their name, they're responsible. If they get approval for 30 watt ERP 12.5 NFM and 15 miles from a specified location and your job site is just outside the 15 miles and you're pumping out 110 watts wideband, and it causes interference so another licensed station, they could be held responsible or YOU could be held responsible for operating unlicensed. Even if they did sucessfully modify the license, and I don't think they would be able to, you could stop using them tomorrow. Then what?
That's asking a really, really, really big favor of the vendor.
They probably told you "it will cause interference" just to be nice. It's nicer than saying some other commonly used explicit phrases.
Second of all, you should be more concerned with interference from the system and other users that may be assigned to those freqs and how usable those freqs are going to be for YOU.
Third of all, modifying a license takes time and it takes money (application fee) and there's no guarantee approval will be granted. My guess is that it probably wont be, at least not without coordination for the simplex operation in a given area. And coordination can cost hundreds. Why don't you just go get a license for the intinerant frequencies. You don't need coordination for those and you can literally get licensed for every single itinerant frequency there is (including vhf and uhf) for $160 for 10 years. That's less than a GMRS license for the same amount of time. They're perfect for construction or job sites because you don't have to pin yourself down to any particular location.