Earlier this week, we had substantial rainfall and I discovered a leak in the passenger rear floorboard. Checked other posts, and it wasn't the wiring boot between the jamb and the door. It appears to be a large hole in the gasket in the corner just above my finger in the attached pic. Can this be resolved by simply applying some GE Door/Window Silicone in the hole?

 

Yup, just dry it out well beforehand using a hairdryer or whatever you have handy.

 

Do not close the door until that silicone dry's. You don't need the door glued when you try to open it and make the seal even worse.

 

No, you have a part missing. It’s a little red pin that is similar to a fender retainer. Just get a new one and push it in. I had the same problem.

 

I looked at mine. That hole is supposed to be there. It's made that way.
Your leak must be somewhere else.
I would look to where that "hole" sends the water runoff. Might be another leak spot.
I wouldn't advise plugging that corner hole. You'll create a problem if the water can't drain as designed.

 

While I was putting down sound deadening in the back of the car it started to rain, so I closed myself in the car and continued to put down more material. The car was completely apart on the inside. Then I noticed water dripping on the seatbelt from the roof. I checked around the roof rack to make sure it wasn’t loose. Then I opened the door and a red clip fell off, I ran around to the other side and it had a red clip securely in place, I put the red clip back into the other side and sat inside to see if there was still a leak.
No leak!

 

Got curious.
Shot some water in that hole. It drains down the inside of the hollow weatherstrip as indicated by the yellow arrows. Most of the water reaches the bottom(big arrow).
I noticed some of the water seeping out of the weatherstrip about half way down. I assume that's where the weatherstrip has tabs that attaches it to the car body.
You could have water leaking to the inside through one of those tab/holes.

 

Yes, but underneath that hole there is another hole in the metal that leads inside the car. The plastic clip grabs the weather stripping by way of that hole and fastens it to the metal hole in the body.
I can double check to make sure I’m remembering correctly, or if you just did that, peel the weather stripping back a little and it should reveal the metal hole.

 

Oh yeah, like a tab hole. Mine was missing the tab!

 

Thanks for the info gio. I can see that metal clip behind the weatherstrip.
Wasn't going to pull mine apart to see how it works.

Just trying to stop the OP from sealing up the drain hole that needs to remain open.
He's probably got a leak around one of those body holes. Just a little silicone on the retainer tabs should fix his problem.