Another update for anybody that is still interested in this.
I contacted a solicitor friend of mine. He thought the whole thing was rather messy and couldn't really understand why a Cross Border Sale would matter so much. He suggested pricing a new Irish warranty and asking the UK dealer to pay the price in full as opposed to the £250 they offered me.
I'm only after getting off the phone with BMW and it looks like I've potentially gotten somewhere. The price of a new warranty, with no excess, is €600. That's for 12 months not 24 as Ireland only offer 12 month warranty. The £250 the UK dealer offered me would cover less than half of this (£250 = €290 roughly). However, the two BMW staff I was speaking to were extremely helpful (John Keary and Craig, a credit to the company, couldn't have been more accommodating). The last time I rang I got a guy that took my details and never contacted me again. They're going to contact the UK dealer directly. According to them the usual solution in this case is for the dealer to pay the full price of the Irish warranty. BMW have taken over at this stage, they're contacting Kearys in Cork and the UK dealer to try and sort it for me. I was told that if I had a warranty worth £2000 but only used 6 months of it then normally the dealer would reimburse me £1500 so hopefully I at least get my new warranty paid for.
Interestingly enough one of the guys I was speaking told me that this isn't an issue with cars as we fall under the same catchment area. For whatever reason the bikes differ
Hopefully I hear some good news within a day or two.