I'd second the idea of a liner bag inside a hard case - in particular I think a cheap drybag (from a discount outdoor store) would work well. Hardcase weather seals can fail fairly easily.
The other important rule for me is: the topbox is empty by default. It is empty space that is either for storing my helmet/gloves while I am off the bike, or for storing the day's grocery shopping when I am on the bike. None of the packed luggage "lives" in the topbox. (Maybe a hat.)
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