No "Bondo" EVER on any area where water might sit/accumulate! "Bondo" has its uses (none that I'd ever consider) but this is not one of them I wouldn't use "Bondo" on my mother-in-law's car!
I am guessing you are using the term, "Bondo", in the general sense and not as a name brand. The only body filler I ever use is the Evercoat "Rage" line and I wouldn't use it for this application.
Use the POR15 Patch and Seam sealer for the window channel or the epoxy putty. I've always used the putty but that is because the Patch is a new product line.
Sand, putty/patch, shape/form/sand, primer then paint.
https://por15.com/products/patch?pr_prod_strat=copurchase&pr_rec_pid=6622112317607&pr_ref_pid=6622112219303&pr_seq=uniform
https://por15.com/products/epoxy-putty