Well, I sure would seal it. It sounds a little late for this, but I coat the inside surfaces with POR15 before putting new metal on and then on a seam like you are talking about, I put on a bead of silicone caulk to keep water from intruding and then use bondo filler to feather the metal surfaces to hide the joint. Since you have already put the new rocker panel on, you could; weld, grind and smoth out the seam, or just use bondo to neatly hide the seam and not leave a way for water to get in.
Sorry about rust, but rust and metal go hand in hand and you can never feel that you have beat it :-& . Rust is nothing other than the metal trying to get back to it's natural state :blink: . You should be on a constant vigle for rust and correct it as soon as you detect it. If you don't, in the words of the Terminator, "I"LL BE BACK"
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Good luck,
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