My company does not reach the limit yet (and it seem the limits are per server, because at freeport it say 0 ships).
My only guess, is that i am too high lvl (lvl 39 right now) to buy a raft or sloop in a free port.... and just get a wrong message.
Anyway, cant be able to buy a boat on a freeport just for the sake of do it, is dumb.