I have considered the issues you listed here. My SubShapeBinder links to the parent container of the actual bound shape. Like all other object in FC, it does not allow circular dependency, so we can be sure the parent container the SubShapeBinder links to is not a parent of SubShapeBinder itself.
When the container of the bound shape moves, the shape binder auto updates the placement. So if the container of the shape binder stays still, from the user perspective, the placement is correct.
However, when the container of the shape binder moves, say by the assembly solver, the placement is wrong from the user perspective. But there is no auto update this time, because the child (the shape binder) has no dependency on its parent (the moved container).
The user has to manually sync the placement of the binder (if that's what he want), by double clicking it. He can then proceed to do some more modeling work, and then refresh the assembly solver. A correct model will eventually stabilized by itself as everything falls in the user desired location.
Other CAD that supports this design-in-context use case has a concept of 'Snapshot', where the context is freezed when brought in, and can be manually synced by the user. This is similar to what our shape binder can be. I have added property called BindMode to allow complete freeze of shape update as well.