Removing these invisible parts would require some changes in the Wall3D class which is already quite complicate. Not really motivating for something that is not visible at the end...
I guess your second question is about the depth (not the width) of some doors and windows which don't behave as expected for thick walls. I would like to try to fix this issue too but it's not easy to find a nice solution that covers all cases. Please see this ticket for workarounds.
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Emmanuel Puybaret, Sweet Home 3D creator
