HOW TO - Install Flashing Boot on Metal Roof 

I am. And even though its not approved to be in contact with rubber, we have never had a problem in the 10 plus years we have been doing it this way.

We have been using it exclusively on our roof boots for over 10 years, never had a problem. I personally have not seen it affect the Dektite boots in any way. In fact we just removed one of our boots in a remodel about a month ago. It had been installed years ago. It was still in perfect shape. We will continue to use it. Exposed fastener metal roofing expands & contracts too much to use something like silicone that has almost no tolerance for movement.