You mean inside the tank? The internal pipe is punctured, inside the tank – and so it leaks as you fill the tank? I didn't quite get what you were talking about, when you talked about prying the pipes off.
I think that you mean the moulded pipe inside the tank. White / natuarl colour? It's an integral part of the tank mould and it doesn't come off. It's bad news if it's punctured, but not a disaster.
If it were me, I would have a go at melting the plastic back together – if it's a small puncture. It'd try it carefully on a little bit first to see if it would work. There are epoxys that are meant to be suitable for fuel tanks, so one of those could be tried too, or as well as the melt, though I don't know how well it would adhere to that plastic (some form of nylon?).
The fall-back would be to block-off the tube outlet, where it comes out the bottom of the tank. Then the puncture doesn't matter. Screw a suitable bolt into the outlet and seal it. You don't need that stuff that the American bikes come with, do you? The Euro bikes don't have anything at all connected to the outlet. As long as you have the other tube acting as an overflow drain, you should be ok.