Just an observation, but look at where the rust is - it's an inch off the roof rib. There's still a white stripe by the rib before it gets really rusty. If it was leaking through the roof seam, I feel like it might travel down the rib, and rot the panel out from there, but that's not where the rust is right now.
What did you have up there for insulation before? I'm wondering if you had a leaky roof hatch that was soaking the insulation, and maybe that's whats rusting the roof.
Test with a garden hose, or set a sprinkler up there and let it run a while, and see what's wet inside.
Otherwise, I think your plan to treat the seam should work just fine.