this is not functionality question but more like conceptual.
I do not understand why there can be in QGIS different CRS for project and for layers. I have worked previously with subsurface petroleum software and there CRS "stuff" was lot more strict in that sense that data was almost always tied to the CRS of the project.
Will the data be prone to inconsistency if there is different CRS for project and layers?
regards,
Marin Mirosevic