Welcome to the forums @mreliptik!
Working with bone transforms can be difficult, because of the different transform spaces available. This should become a little easier in Godot 4, as I've implemented a number of helper functions for taking a Transform and converting it to and from the various transforms in the Skeleton.
I would recommend looking at the world_transform_to_global_pose
function (link) in the WIP pull request and writing a GDScript equivalent. Then, you can take a node in the scene, get its global transform, and then use set_bone_override_pose
and pass the converted transform, which should keep it at the node's position in the scene.
(When the 3D PR is pulled in to Godot 4, you could also use a BoneAttachment node for this purpose, as it can now optionally override bone poses :smile: )