Having ridden in a LOT of rain, I always value a seat-mounted tool bag that is truly waterproof, so I prefer the roll-top Ortlieb Underseat Bag in either Medium or Large size. They offer a variety of similar bags in their product line. These larger bags can roll down pretty small or expand to take other things depending on size, like wind jackets, 3/4 leggings, some energy bars, etc.
I used to use bags made of coated nylon but with various openings like zippers. Sadly, I found despite packaging my tools inside zip-top bags inside the tool bags, vibration caused wear-through combined with leakage of rainwater resulted in rusty tools. The roll-top Orts have been the perfect solution for my more frequently used tools. The specialized tools needed only for longer tools or emergencies are stored separately in the bottom of a pannier (along with a spare folding tire for long tours).
Best,
Dan.