OP, do you use fenders? I ask because I am not sure I have ever seen significantly wet anything in a standard under the seat toolbag, even on very wet rides when I used them. Even when I have locked the bike outside for mush of a day in that rain. (I've spent the past 32 years riding in the Pacific Northwest year round so I have seen wet.) I could see getting close fitting ziplocs for say batteries (or paper items) but wouldn't sweat the rest. I've never seen enough rust to matter.

There are enough products we buy that have small custom ziplocs that I would just set them aside and use the ones that fit my "must stay dry" items.

You can also use that fabric waterproofing spray from REI. Doesn't do wonders, but for a toolbag that is water resistant to start, it doesn't have to. (I am trusting you never submerge the toolbag.)

Edit: as I was typing this, I thought "contact Ortlieb. They could make it."

Ben