The Interlux web site says not to use this product over clear epoxy. Why is that?

The epoxy we ship with our kits isn't the "blushing" epoxy that frightens Interlux so much. We use the Interlux Pre-Kote on all of our painted boats with no problems.

You just need to make sure that the epoxy has been sanded with 120-grit to a uniform gray-white surface, and wiped down with denatured alcohol before you roll on the primer.