Depth of screw holds will not effect alignment.
; If the bore colminates easily within the central adjustment areas of the scope, there is no problem with alignment of the barrel and action. It is common for any action to have from .003" to .010" misalignment of the bolt, action threads and front of action face. Even 40XBR Remingtons, of 10 rifles measured up, the average was .006" off. This is why there are so many 'accuracy' Gun Smiths in the States who 'True' actions.
; Some guns just don't throw the bulletrs where the barrel is pointed. There are a number of reasons for this from bedding, to alignment of the bore inside the barrel - if the deep hole drill wandered then wandered back - common on deep hole drilled barrels, the bore points in an odd diferection. If it colminates well, this isn't the problem.
: The rib might be making the elevation difference. Since you can sight it within the Leupold's normally small adjustment range, it isn't too bad and you've done a good job - lucky in the close grouping with various bullets. Many rifles aren't so lucky. With ribs, there is uneven heating as the rifle is fired, and uneven warpage results. Hunting rifles are supposed to hold 3 rounds close to the sights and fewer will hold 5 - although those also exist.
; Most rifles you buy need to be glass-bedded in the recoil lug area, then, on Mausers the steel tube surrounding the tang screw needs to be shortened or removed. This tube's overlength is a contributing reason most older Mausers and especially Husky's split the tang of the stock. It is not necessarily an overlong action tang that does it - the action's recoil lug area, not being glass bed for a perfect fit, allows the action to rock back on recoil. The overlong steel tube does not allow a tight fit there either, and the whole action moves back, splitting the stock in the tang. The fix is to remove or shorten the tube, and glass the action - then epoxy the split and cross pin it. Much better to 'fix' it before it splits.
; Glass bedding the recoil lug and removing the steel plug eliminates the splitting problem. The action cannot move and then neither actions screws touch wood - perfect - better, more consistant accuracy results!
; It will probably need to be re-sighting after bedding. If anything, it will be more acurate too. If it is already bedded, Great! - that shows in it's excellent shooting now.