We have a mirriad of connectors, seams and notches which add/subtract metal and/or insulation as required and apply a variety of notches to seams and connectors for ease of fabrication on the factory floor.
Some of the options you mention, such as " Roller Allowance" apply only to Oversize seams as you will see if you read the Help file which you referenced.

I think you will find your issue is that you need to understand the interaction between Notches, Seams and Connectors and get them set up as required.

If you post a diagram of what you are trying to achieve I might be able to help.