There are products by Vacaway, Judson,
Releasit that are designed specifically as an encapsulating rinse agent. I believe Pro's Choice makes one as well.
They are low foaming and any residue dries to a nice brittle polymer just like the main encap shampoos do. If you bumped the dilution up a little bit, I'm sure it could save a step on a commercial job instead of misting an encap product, and post bonneting you would probably be able to skip a dry stroke and bonnet. Just a thought..
But nobody that I've heard of has had a problem running any of the above rinses. such as Releaseit Encap
Punch, Judson Low foam Snake Oil, Pro's Choice Crystallizing rinse, or Vacaway's Rinse N Stop through their chem systems. You may want to run some warm water through at the end of the day just as a good measure.