While running AECOsim Building Designer, you only need to go to the reference which you want to have ignore the clip volume and change its Reference Presentation settings to ignore Clip Volumes. It appears that this doesn't work. All the View options do not have any impact whether on or off.
The clip volume setting in the reference presentation dialog does not refer to the clip volume in the active file but rather to the clip volume found within the reference.
You can reference the help. The clip volume flag is meant to work with a reference which is attached using a saved view and has a clip volume defined in that model.
If so the clip in the reference can be turned off or on. However the Clip in the Master model will be applied either way so if any portion of a reference is outside the clip volume in the master the clip volume will be applied.