Make volume buttons only control headphones?
I did eventually get around to solving this using ControllerMate and Multi-Output Devices instead of LineIn.

Using Audio MIDI Setup I created a Multi-Output Device that outputs to both Soundflower and my headphones:



Now use this device for system-wide sound output.

Then using ControllerMate and an accompanying AppleScript I was able to 'bind' the volume buttons on the headphones (I use Apple's standard earphones) to controlling the headphone/speaker volume only:



(Apple Mikey HID driver is what ControllerMate calls the controller associated with the buttons on the headphones)

The AppleScript for lowering the volume:

set volume alert volume ((alert volume of (get volume settings)) - 100/16)
set volume (alert volume of (get volume settings))*7/100


and for increasing it:

set volume alert volume ((alert volume of (get volume settings)) + 100/16)
set volume (alert volume of (get volume settings))*7/100