Yes, it definitely is planned to do this automatically.
In fact I have a hacked together implementation for `scons doc`, which generates the HAL and builds the entire doxygen API specifically for your project.
It's on my backlog of things, I haven't worked on it for a while, and it only works for one device (it's very hacky).
I accidentally published that idea in the docs before I even started the implementation. I removed it again:
I'm always struggling with SCons, since it's APIs are not documented anywhere.
:-(
Niklas