Once you have dated documentation that shows the car was in the country by the Brexit date, e.g. a ferry ticket with the reg number shown, then there should be no impact on VRT charged as this isn't a customs duty. This documentation is required anyway when declaring a car for the past couple of years. Customs duties will be levied after Brexit at port, or point of entry, if Irl/NI customs infrastructure is put in place.

The only circumstances that I can see VRT being affected is if Revenue determine that the OMSP of cars changes dramatically due to the disruption to the market (impacting supply/demand balance) that arises from either logistics issues (ferry port activity, customs declarations delays, etc.) or the higher costs of imports due to the addition of duty on import.