Is any of this stuff going into the 3.6.9 Branch? Cause I was led to believe that this was all HEAD only.
Nope, HEAD only. 3.6.9 isn't broken, so no point in fixing it.

support for more joystick axes for lateral, vertical, and reverse thrust
seprate mouse bindings
multiple joysticks
Not going to happen any time soon. These things require reworking the input code, which isn't going to happen at this time. You'll have to wait for the all new pilot file code before that happens.
Remember that this isn't a replacement for the new pilot file code, but only a standard upgrade since it's already broken and we might as well add a few minor things at the same time as fixing it. Adding support for new mouse buttons, changing the joystick support, and anything else in that basic category, will NOT happen with the upcoming code fix. Valid things that we are looking to add now would be things like the push-to-glide control, or that Freelancer-style mouse patch that was posted a while ago.