You need to do your bone posing by handling/subscribing to the SkeletonAnimation.UpdateLocal
event.
UpdateLocal happens after the animation is applied so your changes won't be overridden by animations currently in progress.
You can also use UpdateWorld
and UpdateComplete
depending on what you need.
Animations only apply changes to bones and properties it keys. If you're actively changing the angle of your bones, you can always keep setting it until you don't need to set it anymore. Even at timescale 0, the animation is still being applied.