Can you put Ardupilot on any flight controller? Some FC's say that they support cleanflight and have no mention of Ardupilot. Is this just because its what's recommended or because it's all that works?
There are pre-built binaries for many flight controllers. 

http://firmware.ardupilot.org/ lists out the different ardupilot builds (arducopter, arduplane, etc.) and by clicking on them , you can see the different versions, then the different builds per version.

This document goes into more detail on the file structure they use for pre-built binaries.