Self etching primer?  You would be working with aluminum then?  I'm just
priming 4130.  I don't think I want to etch that (at least I've not heard of
it being recommended).
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Actually, I was referring to steel parts, which are all that I've used the
epoxy paint on.  I also use the self etching primer on steel parts, and have
never heard anyone say not to.  It's an interesting point, but I just don't
think the "etching" is really going to be a structural issue.  It would
certainly have to be much less damaging than rust.

Rusty