I assume You have a Savage 12BTCSS or equivalent? I also assume it has the typical Savage Steel Pillars, which are the most robust in the industry. I doubt the pillars are damaged enough to make any difference. I believe if You do a normal bedding job, You will get all the performance out of Your rifle it has to offer.
Part of a normal bedding job includes removing some stock material, roughing up and/or punching some drill holes for the bedding epoxy to bite to. Use Your judgment on the thickness of the bedding. When finished, the action will set on 3 metal points. 2 on the front pillar, 1 on the rear. If the bedding covers the pillars, it’s not a problem. Like Dusty says, may even help.
If You haven’t bedded before, follow what ever instructions You use to the hilt.
You can do it !