It's a bit hit and miss, and sometimes it's more finicky than others, but yes, the game seems to work on functionally two dimensional plates, or layers; exactly what does and doesn't count on a layer will vary by map, and sometimes the layers seem thick, and other times quite thin. The boat, for example I'm pretty sure all acts as a single layer, but other larger spaces don't. That is all said with the caveat that I've not seen the code, and only worked off what I've observed from a lot of fiddling about with spell targeting and such. Your experiences may, and likely will, vary, but this behaviour is the best way I can describe what I've observed myself, over the many times I've had creatures fail to be hit by effects they were very much and well within range of.
