They should preffer boats over some structures (mainly docks, enemy towers)
I feel its kinda stupid when I place down a tower close by enemy docks and it keep autotargeting buildings instead of units (boats). It works like this in every case I know about (Barbarican, Outposts, stone towers)
It should deffinetly work just like in regular situation ( Units over structures - when some kind of enemy unit gets into the range its auto-retargeted).