My MDT chassis, which I bought used, was bedded for the same action as mine (Impact). The gun shot like shit. Because the chassis itself wasn't straight anyway (the barrel channel was slightly twisted but not touching the barrel), MDT graciously replaced it at no cost. MDT, as far as I'm concerned, really earned my respect. They never put up a fight, nothing. But with the new chassis and no bedding, the gun shoots bugholes. One thing that got me when assembling the rifle was that I forgot about the washers for the action screws. Went to the range and found the gun not shooting that great (and my bolt was sometimes hanging up on the front action screw). Took it apart wondering if PROOF gave me a shitty 6CM barrel or if I had another bad chassis or something and that's when I realized I forgot the washers (oops!). Rebuilt the rifle and - poof - it shoots amazing and I'm really proud of it. I have since put a Kelbly's Atlas Tactical action in that MDT chassis with a 6.5 CM Kreiger barrel attached to it and it also shoots well, just a teeny bit larger groups than my Impact/PROOF combo now in an XLR chassis (and it shoots the same bugholes in that chassis and I cleaned a few stages in a PRS match for the first time ever.)
That is all to say, you should not have to bed an aluminum chassis. Something in the assembly is wrong or your barrel is done.
I suppose there is a chance your MDT chassis is not mating to the recoil lug well. Frankly that's where I'd look first given the situation.