To reproduce:
1. Open attached project "TestOverrideAnimation.zip"
2. Play "TestScene" scene.
3. Press "space" button. Animation plays, and legs are not moving. In animator you can see that "Action Layer" has "UpperBody" mask applied.
4. Now press "1", to change "Animator.runtimeAnimatorController" to "AnimatorOverrideController".
5. Press "space" again. As you can see, now legs are moving, even though "UpperBody" mask is still applied.

Actual result: "Avatar Mask" has no effect on the animation, after Animator.runtimeAnimatorController was changed to AnimatorOverrideController.
Expected result: "Avatar Mask" works as before, after Animator.runtimeAnimatorController was changed to AnimatorOverrideController.

Reproducible with: 5.5.0a6, 5.5.0p3
Not reproducible: 5.4.3p1, 5.6.0a1

Fixed on 5.6.0a1