Here's a techsheet.
Read under additives on PG.2
Your fisheyes in the base most likely came from surface or air system contamination, the fisheyes in the clear came from the fisheye eliminator that was in the base but not in the clear........ If that makes sense.
The recommendation not to add eliminator to base is given because it will have an adverse affect on the clearcoat adhesion. That's my take on Sherwin Williams stuff, I imagine the same holds true for Dupont.