you will definitely need to create 2 versions of your course as only 1 can have eCommerce turned ON...you could use “100% OFF” coupons if you prefer a single course but all users would need to go through there purchasing process which is probably not ideal. You cannot offer 1 session for free and another on the same course for a cost on the same item. 

Hope that a report of our final solution might help some others. Unfortunately, since as I mentioned in the question, billing is not handled through docebo, so a discount will not work. We invoice separately. We decided to label the course carefully indicating above other content that a fee would apply for sessions not held at our facility. We also made a notification that arrived after registration for those courses indicating that a fee would apply. A reminder as the course gets closer also indicates that a fee applies. These served as an “are you sure?” type notification, and caused some to unenroll or ask to be unenrolled. Finally, because our trainees are technicians, they often do not enroll themselves or handle any travel or registration details. The poweruser at their dealership would do that, so I am finding that I have to send a note to the person enrolling them as well.  It is a bit more of a manual process than I like, but it seems to be working to keep our registrations accurate, ensure that all seats are filled, and avoid billing surprises when technicians attend a class.