Hi all. Had same problem, about 2 inches of water in spare wheel-well and no drain hole.Found the cause in my case and solved it. Water came in from the back of the boot.
I removed the plastic boot lip strip, 2 screws and pull it upwards. Remove removable boot floor.
One at a time, pull side boot trim out and up releasing where necessary and prop up. Head in boot and look rearward. Each side has 2 metal pieces which did not meet up creating a vertical gap. Seal up with silicone and re-assemble boot. Thought mine might be caused by a previous body repair, but seeing others with problem, maybe not! Hope this works for you.