Those drains lead into a plastic 'reservoir' within the plastic trim below the window. The other drain hole (where the spring loaded pins sit when the window is closed) also drain water into the same small reservoir. The base of the reservoir is stuck on with some form of non-setting sealant and can be dislodged if anything is pushed down the hole, or the drain to the outside of the van can become blocked. Use something suitable to squirt a bit of water into the circular, inner drain hole and see where it comes out - should be outside the van. Pop the lower section of trim off and you'll see the reservoir. I'm going to seal the cover on with silicone sealant, although since I pushed them up tightly the window hasn't leaked. I also used a craft knife/stanley blade to widen the 'entrance' at the top of those slot shaped drains you've been working on. Next step for me is remove sliding sections, clean and treat rubber seals with Krytox and perhaps feed some streamer cable into the seals to plump them up a bit.
Another useful thread here