Water intrusion above the 12V battery bay??? Help!

So when I got home this evening I decided to tackle something that I was concerned about- the state of the HV battery fan. As I took apart the back right of the interior to get to it, I noticed that there was moisture on the inside of some of the trim pieces where I wouldn't have expected it- but I discounted it because of how much moisture had been in the car after having it detailed.

As I got further in though, to my annoyance it started to rain, and I had to stop (since I was working in the driveway). When it let up a bit and I went back out, I was dumbfounded to find a lot of water splashed over the 12V battery. At first I thought it was from the lift gate being open when I had been working on things, but it was no longer raining and there was still water dripping down. After getting a towel to put over things to catch the water, I tried to track back where the water was coming from, and found that it was dripping from a formed hole on the underside of the upper 'sill' (along the side of the glass in the lift gate) from inside the body from sources unknown (well, I know the water was coming from the rain, but not how it was getting into the car...)

I managed to get a picture of the hole- you can see if you look close a droplet of water on the left side of it.

Where the heck is this water coming from? How is it getting into the body? And how do I stop it so it doesn't cause a short or worse?

 

Yikes! Those pictures of the cracks are ridiculous. I guess that I need to pull off the roof trim and see if I can find the cracks on mine and try and seal them up. I wonder, would using some kind of expanding foam sealant be even better than just the silicone sealant? If there's a way to feed it into the crack it would help seal it up on the inside too.