Fix Overlaping volumes in Acts tracking geometry

The addition of the Beampipe to the Acts tracking geometry resulted in an overlap of the Beampipe volume and of the Pixel one. This caused the wrapping to not be performed correctly resulting in an inconsistent boundary between the barrel and positive endcap (see picture bellow).

Decreasing the Pixel envelop from 5mm to 3mm resolve this issue :

This also change some jobOption to properly account from recent geometry changes