Yeah, JBWeld has steel powder mixed into the epoxy as a filler.
If it isn't primed and painted it will develop rust spots.
An alternative if you are worried about possible rust dots
is an aluminum powder filled epoxy like those offered by http://www.hypoxy.com/
Also important to remember to chamfer the top and bottom of the hole being repaired
so the chamfers act as locking tabs, when filled with the epoxy putty.
If I remember correctly Marine Tex used to have a display at boat shows where they'd used the stuff to repair an engine block... I wouldnt' hesitate to use in for your purpose... If you're hesitant, just do a small spot and see what results you get. I'd use the gray color instead of white (if they still make it...).