Hello members of this community, 

Allow me to elaborate my question with the diagram below. 
When RnD define a spot weld using the Fasten App, its location is defined on the surface of the pilot part. The TCP on the welding gun is on the surface of the lower end's cap which then is used to position it onto the location of the spot weld.

In the diagram, the TCP location is aligned to demonstrate this point. In such an example, we will measure a larger clearance than in reality as the gun is displaced by an amount equal to the sum of the sheet thicknesses.
In reality, the cap of the gun will lie along the bottom sheet part (highlighted in torquise). 

What is the best way that one should consider this while performing simulations ? 

In our Delmia V5 days, we would have an extra geometry of the lower gun end and cap that would be displaced a standard 10mm in the downward direction which we would hide/unhide when measuring minimum distances. 

The Additional Parameters in the Analyze Targets command is also a great functionality for displacing the gun but only when doing static studies.