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I noticed in Edit mode on my bone that I could rotate a bone with R+X or R+Z entirely as expected, but in order to rotate along the Y-axis R+Y simply has no functionality. Instead I'm forced to memorize a new hotkey, Ctrl+R to accomplish this same task. Why does the hotkey R+Y merit this replacement? I will need a good reason, since I believe that no appeal to local vs global axes has anything to do with this. Specifically I'm expecting Ctrl+R to contain some extra functionality I'm unaware of.

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If you look in the Properties/Transform panel you will see that individual bone transforms are defined differently to other objects; they have a Head location, a Tail location and a Roll angle whereas other object types have Location and Rotation property sets. The Roll Angle can be used to influence how they deform when e.g. IK Chains are animated.

The rotation hotkeys in Edit Mode will spoof the usual effect by changing the Head and Tail transforms for Bones rather than changing the Rotation properties like they do for other objects. If your bone happens to have its main axis (from the fat Head end of the diamond to the thin Tail end) aligned to one of the global axes then the more relevant Roll Angle hotkey is required.

bones at various angles

In my Edit Mode example here I have some bones along each of the global X, Y and Z axes and one that is not aligned to any of the axes. Those on the X axis only respond the the Y and Z rotation hotkeys, those on the Y axis only respond to the X and Z hotkeys and those on the Z axis only respond to the X and Y hotkeys. The diagonal bone responds to all three rotation hotkeys. All of the bones respond to the Roll Angle hotkey.

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