Hey everyone... I'm restoring an aluminum boat and right now I am trying to decide what to do as far as coating on the inside of the new transom to prevent corrosion. I have some self etching primer and also some Zinc Chromate. I was going to use the Zinc Chromate but I got to thinking that any electrolysis may just attack the zinc and remove the coating. So I don't know what to do.

Any wisdom would be appreciated.

If the transom is aluminium then it will oxidize and that alone will be very corrosion resistant. Aluminium doesn't need to be painted for corrosion. If you want to make it look nice with paint then sand with 220 lightly, clean and etch with vinegar, and prime with Chromate soon after, dry and paint. I am sure you know zinc chromate is extremely toxic be careful with it.