That's a good shout, when you say fit it with a female cup what product do you mean?Well I'm totally inexperienced but strongly suspect it's GRP. The only EPDM I've handled was sort of like vinyl cushion floor to the touch, and I'm sure you know what a fibreglass bath feels and sounds like. Personally I agree with cdbe's suggestion of capping it. Provided it's not leaking at the moment and you cut it down to ~3 inches or so and then use a female cap I can't see how that's any worse than patching a hole and it's a whole lot less work and requires no expertise.
You could even fill the inside with the dreaded expanding foam so you aren't really losing anything in terms of insulation.
Also the builder got a durgo valve to cap the soil stack on the inside so we could lower the soil stack and still use it for sink and dishwasher waste. Presumably this is irrelevant to the capping of the top?