
Here spineboy's back thigh has been scaled on the X axis which elongates the thigh, shin, and foot. The shin and foot are scaled on their local X axis, which is probably not the desired result. In this case, scale inheritance can be disabled on the shin so it is unaffected by the thigh's scale.
Here is how it would look with skewing transforms (bones are hidden):

The whole leg is stretched in the direction the thigh bone is scaled, instead of using the local axes for each bone. Because they are always scaled in the direction of the thigh, as the shin and foot are rotated in relation to the thigh, they are scaled by the thigh differently:

Skewing transforms can be useful, eg to make multiple bones or a whole character squash and stretch, but when nonuniform scaling skews a bone's coordinate system the X and Y axes are no longer perpendicular and many things become more complicated. Eg, a 360 degree rotation is actually an oval, bone compensation is not possible because the skew can't be represented by SRT, disabling inheritance of rotation and scale is expensive in the runtimes, and more.
It's actually easy to change how Spine computes transforms and I have already done it, but all the loose ends need to be handled before it can be released. Also, we would need to decide whether we change how transforms are applied and potentially break projects that use features that work differently in the new system (scale, flip, inherit scale/rotation, etc), or do we allow either the old or new mode to be chosen for a project. This would prevent existing projects from breaking but mean all the runtimes would have to support both ways, which is a pretty big burden.
Thoughts are welcome!