From my experience I think the factory sealant on the inside at the font is well... A tad crap.

Mine was leaking from the front gutter internally, I also had rust keep flaring up on the usual spot (drivers side corner) so even when I sanded back to steel and repainted it was back in a month or so.

I got sick of getting wet pants while driving in the rain, pulled out the hoodlining. What I found was there were sections of the internal join where the sealant had failed or was never there in the first place. I replaced this with lots of sikaflex that I then used a finger to really push it into the join. Since then not only have I not had anymore leaks I've also had no new rust (well not in this area anyway).

A couple of other things I've noticed in a lot of vans at shows etc.
Many seem to be missing sealant in the body joins (ie ute van seam)
Many have great paint that is extremely thin in the gutters themselves.
Both of these issues are always going to cause rust.

I strongly recommend against always parking in sheds or never driving in the rain. We're talking about glorified plumbers vans that need to be enjoyed, not oil paintings.