As long as no part of the barrel and nut are not interfering with the stock then it shouldn't make a difference. The nut should be torqued to make sure the lug is in correct position. Also after the barrel is head spaced correctly a free float check must pass or more channel material must be removed to fit the action in the bedding where it belongs.
As far as the lug bedding in the "test" action, might be best to re-bed because when the action is torqued in the new pillars it is most likely going to move a little. Removing a little from the old bedding should be enough. Then installing the action and snuggling it down will make a perfect fit.