The current bolt length calculation does not include the parameter "flange offset" as this affects only the visual aspect. We have to manually adjust the flange thickness in the lapped flange to include a stub-end or collar, and create duplicate lapped flanges to mate with every possible.
Having the bolt length calculated with the flange offset included would solve many problems. This should be switched on or off in the project setup, so that existing projects that have the manipulated flange thicknesses are not negatively affected.