We've always got through OK by booking as 2 cyclists (Fishguard/Rosslare, Larne/Troon, Calais, Dieppe, Dunkirk, and some others I forget now). Some websites have a bizarre limitation of only one per bike per transaction, I think we got around that by having 1 cyclist and 1 foot passenger IIRC.
Anyway like others, it's never been a problem in practice when we cycled up to the counter.