I have some odd issue with layer muting and payloads.
In this very basic example I have a shot USD with an animation layer which consists of a payload to to the cube and a reference to the animation of it.
When I load the shot.uds and mute the animation layer everything looks normal (the cube no longer 'exists' ). However, when I load the reference to the static cube again as a payload the animation is still occurring. If I load the cube as a regular reference the cube is static, as I would expect.
The idea here being I want to mute the layer and rebuild it rather than retain what was there before.
It seems 'muting' isn't a state that persists if the stage is edited so the alternative is indeed to 'not load' the sublayer(s) one doesn't want. Not very USD but I suspect it's quite a common strategy