If you can see rear hatch rust, there is probably 75% more that you can't see, under the seal.
This was 100% invisible:
This "perfect paint"……
…was actually completely lifting off due to rust and water incursion…
My recommendation is to acquire a new seal, remove the window, scrape the large chunks of rust out, wire brush the rest, and use a Rust-Catalyzing Primer on the remaining metal. After 24 hours, you can top coat this with a color close to your car. I have one spot on mine that I have to inspect every half a decade or so.
Here was 2012:
And 2016:
After treating with a wire brush, RCP, and a top coat of Rust-Oleum paint:
Here is my favorite catalyzing primer, available from O'Reilly's or Amazon:
https://www.amazon.com/Dupli-Color-RF12 ... B001DKR4BE
You can spray it into the cap and use a watercolor brush to apply it locally. It converts the iron oxide (rust) to iron phosphate (or similar; inert) so you can treat it like a primer once it's dry.
Good luck, and let us know if you have any questions!
Robbie