OK, your good to go then :-)
Just some comments to your original questions:
1.
Im not familiar with this "merge" option and how it may or may not be effected in sheetmetal so i cant help you there.
We normally use publish/copy geom.
2.
The ext_ref_scope is a setting that defines what items can be used as references when you are working in Creo.
Lets Say: If your intent is to "drive" your entire design from the skelletion then it makes sence that only the skelleton can be seleced as references when you are creating a part or assy.
3.
YES
If the design is not documented properly and/or the users are not familiar or trained in the top-down design method then will get into trouble.
And you know who they will blame ;-)
Hugo