the customer note about equal clips not being recognized as equal is correct. The issue is that the engine code that tracks animation overrides uses actual equality, but in this case, there are two identical animations built into the build. So even though the source asset was the same, the resulting asset is not. The workaround is to change the user code in AnimationClipOverrides.cs

adding this new method:
private AnimationClip GetMatchingClip(AnimationClip clip)
{
foreach (var clipPair in Controller.clips)
{
if (clipPair.originalClip.name == clip.name)
return clipPair.originalClip;
}

return clip;
}

provides a way to take a passed in clip, and find the clip on the current object that has a matching name. Then the [] operator in that same file becomes:

public AnimationClip this[AnimationClip clipKey]
{
get
{
AnimationClip val;
var clip = GetMatchingClip(clipKey);
_overridden.TryGetValue(clip, out val);
return val;
}
set
{
if (clipKey == null) {
Debug.LogError($"Trying to assign clip {value?.name} to null key.", Controller);
return;
}

var clip = GetMatchingClip(clipKey);
if (value == null) {
_overridden.Remove(clip);
} else {
_overridden[clip] = value;
}
}
}

With these changes, the game works.