Seam sealer on underside?

I'm just going through this process now too. Floor plans are in and I was thinking to use 3M's seam sealer both inside and underneath. Primer first, then seam sealer, then truck bed liner.

If you seal the seams completely, would there be concerns, or does condensation still allow water to be present under all of that?

I don't think there would be concerns in your lifetime. I am using Dominion brushable seam sealer on mine and I really like how easily it brushes on. It dries quickly and cleans up with mineral spirits. I am sure the 3M is the same. I have a can of it too but I haven't gotten to it yet. I will before it's all done.