Hello. Yes, you are right. Most mappings by you are fine squared.
What I don't understand is your explanation of using a layer.
Adding a layer means that it is above ground level, 
layer=1 . A Bridge  crossing a waterway.
layer=-1.  A ford crossing a waterway
Layer=1 added to a building, Example . roof above a fuel station. 
The alignment you make is overruling the mapping of previous mapper, but underground or something when you add a layer=-1
Don't be afraid to change something when you are convinced that your view is correct.

Best regards