Given a mesh with non-uniform scale and custom normals, attempting to join that mesh into another mesh that has uniform scale will mess up the custom normals.
If the custom normals are being created by a modifier during the build process, applying all transforms beforehand should avoid issues with the normals, but this could cause issues with other modifiers that are applied during the build process.
Hopefully it will be possible to scale the custom normals before joining the meshes so that the end result is the same.
This isn't technically a bug, since this is Blender's default behaviour when joining meshes, but we may be able to do something about making it work better.