So this is something that we get from time to time too and it usually presents itself as "Hey I had my gun in (insert stock here) and moved it to your (insert MDT chassis here) and it doesn't shoot the same/as well. Is this normal and how do I fix it?"
Now granted, I do not have the same experience as a lot of you guys/gals out there and have never ventured too far down the glued BR guns rabbit hole, but there is no way that a barreled action in a stock should shoot the same as in a chassis, in my opinion. When you inlet and bed a good stock, you are basically guaranteeing contact between a good portion of the bottom of the action and the rear face of the recoil lug, maximizing your contact. Furthermore, if you have any variation in the action or stock, that will be taken up by the flex in the stock as it is cinched down with the action screws.
Now to compare this to an aluminum chassis, you don't have the same forgiveness that you'd get with a fiberglass or wood stock. If there is any variation in your action, the aluminum doesn't deform and wrap itself around your action like the bedding compound in a stock will, however, it generally provides a much more rigid and robust surface to mount against. Now granted, we take some extra measures when inletting and designing our chassis to account for action variation/concentricity, potential metal deformation and correct chassis contact points, but as
@bourbonbent said, tooling wears out and no two chassis are perfectly identical.
What my point is, is that when switching the same barreled action and load between a stock and chassis (or vice versa) you will have to make some adjustments due to the interface between the action and stock/chassis, as well as the induced harmonics. I don't think it's fair to say that a chassis or a stock will shoot better simply due to the fact that there are too many variables!
Just some thoughts on the topic, but I suppose I am biased too