Well, never heard of a throttle body and an ECU ever needing to be "a matched pair". How is anyone going to change one of those items ever again if they always have to be replaced together. Compatible, yes, but a matched pair? Sounds like antiques roadshow. Maybe they mean that a new ECU needs a newer design throttle body
Are you paying for this or is this a warranty job? To replace a throttle body, it does nothing to repair the fault and then they say it needs replacing again with another one sounds novel and is ok as long as you're not paying for each one. What's the reasoning?
ECU needing replacement might well be needing to bite the bullet as you're between a rock and a hard place but check the car out thoroughly before paying any bills and driving it away