Water in spare tire well?

This can be annoying to do but when I've had to find leaks I get a helper, they get in the trunk with a flashlight, and I go outside with a garden hose. Then you apply water around the trunk while tapping the lid so the person inside can follow where you are with the light. If you don't see anything there then you try other areas, like the areas the hinges bolt on. If nothing is there, take the carpet and everything out of the trunk. Now put the car up so you can get under it with the hose. Yes, the hose user is going to get wet. Now sprinkle something like carpet cleaning powder or even better comet cleanser (it turns blue when damp, but stinks like chlorine if you don't clean it well) around the trunk on all the seams. Then go underneath, spray one area for a few seconds, now check the powder for signs of dampness or wetness. If it's getting through a body seam you will likely find some rust, there as well. Clean it all off and apply seam sealer to the leaking area, both inside and out.
It might take a day to find it.

I know I am not the only one who has had a spare tire well with after in a 90's Pontiac. You can find postings on the internet.
Someone out there may find their answer in the possibilities I have already ruled out.
So - I will elaborate on my issues.

Adding to my original query.
Forget the seam along the bottom of the spare tire well. If this was the issue - the water would drain back out, not get a few inches deep!
With the exception of the welding along the bottom for the tire retaining anchor - the entire well appears to be a seamless stamping from the trunk floor down.

My best guess is that there is water coming up into the driver side rear fender (when the car is driven in the rain) leaking through to the underside of the carpet and making its way into the spare tire well.
Has anyone seen such an issue?

I have never stripped out the carpet which lines the trunk floor and covers trunk insides of the fenders. Perhaps there would be signs of the leakage path.

To complicate troubleshooting - but making this problem easier to live with.
I am living in Santa Clara CA. Starting 2 weeks ago it has been raining a lot - and will continue to do so for the next two weeks or so.
You may have heard that we are in a 20 year drought. So - I can go the better part of a year without driving ion any appreciable amount of rain! So - when it's not raining - I am not getting water into my spare well.
I have never been able to get water into the trunk by spraying the car up top, car washing, etc.
I have not tried to get under the car and spray up.

Steve W, sounds like good advice. Makes a home DIYer wish he had a lift!

I am about to drive 1,000 miles round trip to San Diego (from Santa Clara) and anticipate much will be in rain. So as a temporary fix, I have fashioned a drain replacing one of the oval plugs on the floor of the spare tire well. Eventually - I would like to get to the cause of the water input. Just will not be within the next two weeks.

Okay, how about pulling the carpet before you go? Might let you find out where it's coming in. There are weld seams all around the trunk floor that can leak as well as at the wheel well seams and trunk floor edges. With the carpet out the path should be obvious as it will leave staining on the paint and sealant areas. I've done the routine with the vehicle on the ground, on ramps and on a lift. The lift is nice, but the other ways worked. I've even driven one through a car wash with the undercarriage spray before to look for odd leaks.

Good advice. I have pulled the carpet.
Placed the spare and jack storage in a heavy-duty plastic bag. Any water that gets into the spare tire well will exit through my improvised drain, get no deeper than near 1/4"
Several hundred miles of travel through the rain that is expected - should result in water entering the trunk. Hope to see tracks and wet spots indicating the problem entry points.

Let us know what you find. We'll be here waiting.