Luis
There are various ways to deal with "skid" stress interfaces & there exists different opinions on the same too.
I generally prefer either of the following:
a) Model your system till the interface with vendor & pass the displacements at scope break flange to vendor so that the effects of your system will be taken care of in his skid analysis.
b) OR model the skid with some suitable assumptions (or with the skid GA ; if you have that) along with your scope piping & pass on the loads & moments on the scope break flange to vendor for his approval.
Also, refer attach
this for some more light on this "touchy" topic.
Hope you've a good time breaking your head with the MECHANICAL DEPTT.