Most stocks are finished before the owner decides to do the bedding job. The bedding compound will not stick adequately to the finish, so you end up removing finish where the bedding will go and inletting grooves or channels into the wood to give the bedding a foothold.
You can bed a bare stock, obviously, and probably get better bonding and enjoy the advantage that no gun oil will have yet worked its way into the wood where you want the epoxy to go. However, once bedded, in order to finish the gun you will have to mask off all the bedding. The finish will prevent the gun from fitting back into good tight bedding, plus it won't be hard enough or stick well enough to the bedding compound for consistent or permanent results.