Another owner on this forum, @Matthew Yates, also has a problem w/ water pooling in the transom locker. That owner didn't mention ineffective drains.
On that problem, the bottom surface slopes down to the bow of the boat, making any aft drains, if they existed, ineffective. Is that also the problem here?
An image would be helpful.
There are one foot square colored floor tiles that create an elevated platform for this purpose. A drain to the bilge could work. Has sealing the intrusion been attempted?