This is what I have at the moment, so basically I could pop the intake side off, and refit the vent and just keep it under the seat ?The two holes under your seat look to only be in a piece of aftermarket trim panel which could easily be remade with only the outlet hole. If as @oldiebut goodie says the inlet is taken from under the seat base no additional hole is necessary. However do make sure that a grill is fitted on that inlet to prevent items entering the heater and fouling the fan.
Thanks for all your help, bit disappointed in the conversion company to be honest. Trying not to think about what else might be wrong.