The rust started under the Rubber window bead. Probably areas of steel that got scratched during the assembly of the window or subsequent window replacements.. Never seen an Autoglass fitter re-spraying any areas under the seal!
Unfortunately, the only long-term fix is to take the window out and grind down to bright steel (if there is any left) then etch-prime and paint.
You can peel the rubber trim back and get a dremmel in there, but there will still be areas of rust that you can't get to, and they will soon start to spread.
My CE had water comming in through the front windscreen edges that had rusted away. Luckilly, there was enough steel left to support the glass and it was only after the window fitter pointed it out and "fixed"n it with loads of goo that I had a dry car for the first time in 5 years!