For context, I have a character that I rigged in 3ds max using CAT, ported him into blender as an .fbx, and have been reorienting his bones in edit mode after they loaded into blender perpendicular to their original alignment in max. Following the advice of another post, I have been slowly changing the roll value of each of the bones until what I assume is their local z axis roughly matches the global z axis in blender. What effects does the bone roll orientation have on the bone orientation in a game engine like unity?
Bone roll is important when using constraints, drivers, curves editing, clarity of animation programming; but after an animation is done and saved as Fbx, generally it's baked, so that a "pure" rig (a rig without constraints, drivers, control bones: made with deforming bones only) is exported.
This behaviour is set in the Fbx exporter preferences (bake animations, deforming bones only). The baked animation will correctly perform in Unity with any kind of bone roll.
Be aware that if you change the bone roll every previously made animation will be broken.
A common good practice is to set the "main" rotation of a bone as positive X axis.