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.