On my 340, there is nowhere near as much caulking at the rub rail and anchor roller housing. In fact almost none that I can see. I have no leaks in the area as well.
I was putting my dinghy in the water today and remembered your post. My boat goes in this week, I thought I could get on the boat but there were no ladders available to climb up there. (everyone locks them to the stands, go figure) So I took a few ground level shots for you to see. Not the clearest of pictures but it does show the area for you to compare. When I get on the boat I can get better pictures for you.
If your rub rail is newly replaced and sealed you shouldn’t need that much sealant again.
And the bottom of the box, as you referred to, doesn’t touch the hull on mine as well.
I hope this gives you some help in seeing what others have.
