My take on this is the company is in northern Ireland.
When working for this company does your job entail you travelling south of the border on business?
If you are required by your employer to travel south of the border representing them then they should pay the VRT.
If you only represent the company north of the border but utilise the car south of the border for personal use (going to and getting home from work) then you will have to cover it.
Either way the VRT is supposed to be paid, it is a discussion you need to have before signing up to the company car.
Not sure if their is some legal loop hole here.
My brother used to work for a company in Armagh.
He covered Munster and south Leinster in a northen reg.
About 18 months into the job he was stopped in Tralee by customs and the car was impounded.
He rang the company and they paid the VRT straight away and he got the car back.