I hadn't thought of using silicone spray on the seals - might have to give that a go. Judging from the state of my old lock on the nearside, I'm thinking that water is getting in either the way you're describing, or it's getting in around the curve of the wheel arch. I've got a slightly larger gap there than in the rest of the door, so wondered if there's an issue around there. If it's that, I have no idea how I'd fix it...
If it's what you describe, it might just be a matter of adjusting the strike plate - they go up and down as well as inwards and outwards and a tighter fit might just be what sorts it.
Looking at the sills, it's worth checking to make sure everything is flush. Where I've pulled the carpet up a few times to put towels on the sound deadening, I noticed that when I pulled the carpet out from under the plastic trim, it lifted the trim out of its retaining clips and wasn't back in properly. Be warned - you have to go all the way back to the boot trim if you want to do it properly - I tried to manhandle it back in, but the plastic trim that's level with the seat backs has to slot into the trim lower down, and it's really hard to get everything where it should be and not end up breaking clips etc. if the upper trim piece is still in place. Then it's a matter of working the rubber lip on the sill over the trim piece.
Utter ball-ache that was to do today. Hands are raw now.
I did that a couple of years ago, but have noticed recently that my shifts still feel pretty notchy. Starting to think about changing transmission fluid, as it's never been changed...