If a plane leaks when flying through rain, it will also leak sitting on the ground parked outdoors where, statistically, it will see far more hours of rain than when airborne. After a while, it's going to stink like a cesspit. I know, I used to fly Tomahawks which would have 1/2" of water on the floor (and stank accordingly).
I'd get the door seals fixed.
If the door seals are that bad, chances are the filler cap seals haven't been looked at in years. I once drained about a litre of pure clean water out of a Tomahawk fuel tank; this is not condensation (not physically possible, by at least one order of magnitude), it's duff seals allowing rain to get in. Now, think how much more rain will get in at 100kt...
Naturally, all these were on a CAA Transport CofA.........