The contractor's welders are bound by the WPS. If the WPS limits the root to 3 mm, that is what must be used. If the WPS states the root opening is 3 mm +/- 8 mm. that is the acceptable range the welders must comply with.
If the root opening does not comply with the WPS, the inspector should generate a NCR. Boot the issue upstairs and have management address the problem and propose corrective action.
While the root opening (root gap) is a nonessential variable, all nonessential variable must be addressed by the WPS. The WPS can be revised, but the change does have to addressed by the WPS. The welders and field crew can not arbitrarily modify or ignore the nonessential variables.
Good luck - Al