Epoxy primer is only effective if applied to bare metal, so put your Raptor right over the seam sealer.
Just a thought... why not just paint it instead of urethane bed liner? It's cheaper (single stage vs Raptor), it's far easier to apply, far less mess and can be removed
on purpose a whole lot easier than bed liner. Bedliner is not good for sound deadening if that's what you're after.
No harm in putting bedliner under your truck but I don't see the benefit. Your truck, you do what you want.
