You're right that the aerial should drain via the plastic tube. It's the same principle as for the sunroof (that's the larger plastic pipe you can see in that pic).
At the ends of the plastic pipe, they go into a rubber thing that's stuck into the bodyshell. That's the spout that directs it out through the body panel. The rubber spout has a set of lips on the outside (this design is referred to as a 'bladder' in industry) that's designed to work as a one way valve, letting water to flow out, but not back in under air pressure (e.g. when the car is moving forwards and wind is blowing up into the rear arches).
On a 4g, the aerial and sunroof have separate bladders, from your pics it looks like on a 3g they're shared. Anyway, it's common for the bladders to be blocked on 4g's now (20 years of crap accumulated in them) meaning that all the water backs up in the pipe and because the rubber has got old, there's no real seal around the pipe, so it just overflows through the join and into the boot.
Pull the pipes out of the rubber spouts and have a look inside. If there's any crap, clear it out and make sure you run through the bladder with a bit of plastic coated wire, to ensure it's properly clear.
I reckon that's the most likely cause of the water in your boot. Either that, or the seals around the rear lights.
Try the bladders first and if you still have water in there, then take the rear lights out and see what you can find.
nb: I noticed this week that the drivers side rear light on my 3g has a few mm of water in it, so that's leaking on mine
) Waxoyl doesn't apply evenly and dries and cracks with age. Rubbish in comparison, for cavities.