Okay…
Is there like an “apply rotation and scale” but for bones
No…
How do you align to an axis AND fix bone roles?
First you need to be able to see what the axis of each bone and which way it is pointed…
Select your Armature > goto the Properties Panel > Select the ‘Object Data Tab’ (the little man icon) > find ‘Display’ Panel > check the box next to Axes… (should say Axis… but who cares)…
Now when ever your in Edit or pose mode you have a nice XYZ icon to show which way the axis are pointing on your bones
Now the easiest way IMHO to edit the bone axis is you have the Right hand tool bar open press"N" to toggle it on or off …
and find the ‘Transform’ Panel > ‘Roll’ slider… and move or type into that slider to adjust the bone roll…
They don’t have a location. rotation and scale like an object does.
No… I will have to disagree… I’m not at all sure where your getting this idea from… all three of these factors effect bones… each individual bone has a Location, Rotation and Scale Matrix associated with it in the underlaying software… just exactly like Objects do… they could not operate in 3D space otherwise…
And in fact… Bone Roll is many times more important to Bones and Armatures than it is to Objects…
Bones have to be aligned with one another to work correctly…
not paying attention to Bone Roll is the quickest way to achieve Gimbal lock and bone flipping in the middle of an animation… Good Bone Roll Alignment will definitely insure these conditions are lessened if not all together avoided…
I highly recommend that you go watch Nathan Veghdals excellent “Humane Rigging” series…
https://www.youtube.com/playlist?list=PL58E9A0927AB357EF
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