When I force build entities over water, they get landfill placed under them. The spider bots are either incapable of recognizing it because of the entity over it, or are incapable of building landfill in general.

They are actually currently incapable of building any tiles at all. The spiderbots need to get a path to each ghost they build, and it was often impossible to find a path to the landfill ghosts, leading to the spiderbots getting stuck continuously trying to request impossible paths.
That being said, they made some improvements to the pathfinder in 2.0 specifically for spiders, so I will look into this again. I've also got a few new tricks up my sleeve for them to use, so it might actually be possible now. Not the next release, but I'll see if I can get it working for a future one :)