read vehicle combat rules.
I did! There's nothing mentioned of what you talk about! It took me following the path to Object Immunities, at which point I saw where they talked about items normally have to be directly targeted. Given that you are directing me to the vehicle rules, I suspect you actually didn't read it yourself and are getting this from someone else.
However, your problem is solved by reading the section on "Areas":
Some effects occupy an area of a specified shape and size. An area effect always has a point of origin and extends out from that point. There are four types of areas: emanations, bursts, cones, and lines. When you’re playing in encounter mode and using a grid, areas are measured in the same way as movement (page 463), but areas’ distances are never reduced or affected by difficult terrain (page 475) or lesser cover (page 476). You can use the diagrams below as common reference templates for areas, rather than measuring squares each time. Many area effects describe only the effects on creatures in the area. The GM determines any effects to the environment and unattended objects.
It's up to the GM as to how something would be effected by something like that, so you can totally say that a wall of fire would affect a ship that is going through it, RAW.