I've asked around the town, and apparently this chap (assume its the same guy) has a reputation for being unreasonable, with some of them preferring to take their cars to the Limerick NCT test centre instead, so they get treated fairly.
Ben from
www.mr2-ben.co.uk was helpful on email today, he took my chassis number and confirmed its actually a 12/90 import black T-bar rev1 G-Limited 3SGE manual engine, and would have come with a 3rd brake light as standard. I'm going to order one and fit that. Its crap really because common sense is to just disconnect, rear window brake lights are not required by law!
The problem is reporting an NCT centre for being too harsh is no drama for the operator of the centres, they will be thankfull its not being too leanient.