Suggest you read up on Korth Group or Leupold website. It has some good explanations on the topic.
Here is what I learned. Drilling scope holes perfectly in line with the bore center line is rather an art. Mass produced items may not meet this "art" definition.
Shimming may be an option to adjust for vertical alignment. I have used shimming under the rear base on a couple actions. Also you may need significant horisontal adjustment.
The goal is to keep your scope centered because it gives the best optical picture and provides you maximum adjustments. First you either optically center or mechanincally center your scope adjustments. Then you can bore sight to see if you need to shim. For example, if you see the recticle well above the target say at 25 yards (when looking through the bore) what you need to do is shim only the rear base. Also, it is important to consider windage adjustable bases (leupold style) to account for the errors in drilling holes in relation to the bore center line. The best way to reduce stress in the scope when doing this is to use burris zee rings with inserts. You can also play with vertical using those rings as well.
If you do not need to adjust in the field then most of todays lower end scopes (such models provide a lot of adjustment) and will provide enough adjustment to get on paper to sight in. The cost is perhaps less than optimal sight picture and reduced ability to dial in when out in the field. Hope this helps.
Elky.