I think both have merits. I roof top, right way up on the launching trolley so boat is supported as it would be on a trailer. I think the car's suspension smooths bumps better then a trailer. Probably costs more in fuel because trailer sits in the cars wind shadow and you are speed limited to 60.
It depends a lot on your car. I have an Octavia estate and I can get it on and off o my own though these days I welcome a second pair of hands.
is there a preference to roof top vs towing via trailer, wondering whether to shell out for trailer particularly in terms of boat care etc thanks Steve