Hi @alex.van.canneyt. We can not change the natural directions of geometry in the models without basically recreating those models. And most geometries have sort of internal ID's assigned to them by the design software, to ensure they can be uniquely identified from all other pieces of geometry, and we can not change that internal ID. If both models were saved from the same base model, then the same face in both models may have the same internal ID. What really needs to happen when you replace a component in an assembly, and the new model is not aligned the same was as the other model was, is to edit the constraint object itself, not the geometry of the model files. If you had a Mate type constraint between the Faces of two components, then you replace one of the components with another component from different ancestry, it does not know which face of the new component to replace that side of the constraint with, because none of the faces of the new component have the same internal ID as the face of the previous component. And I have heard that sometimes when you mirror geometry, some aspects of the newly created geometry that was created may have some different direction(s) than the original it was mirrored from. I don't really know why.
We do have the ability to assign custom names to some types of geometry within parts (not in assemblies), but those names that we can assign are not the same as the internal names of the geometry assigned by the software, so that would not help in the manual process. It can sometimes help when replacing components by code, and then trying to fix existing constraints (if any were broken), by trying to find the equivalent geometry object in the new component by the custom name that we assigned to both the old and new components before that point. But this is a very complex process, and requires a lot of preparation and knowledge of both models. That situation of replacing components and sometimes the constraints getting broken has been a major pain for everyone since the very beginning, and I don't think that anyone has a 100% universal way to fix this problem from ever happening again. There are some things that can help lessen how often it happens within certain fully controlled sets of model files, with enough preparations, but I think entire books could be written about how to do those things. Sometimes, when there are multiple designers involved (past & present) in creating all the model files, and years worth of pre-existing model files that you may be working with, including content center and/or library models (which are ReadOnly), it just doesn't make practical cense to attempt to prepare every model file individually for the possibility that you may need to replace one with another in an assembly, and try to maintain all their possible types of constraints. It can be a monumental endeavor to attempt it from that direction.
Wesley Crihfield

(Not an Autodesk Employee)