If the gun has extra holes, it generally doesn't bother me. What does bother me is recoil pads and crappy bores. Many times a couple extra holes can be beneficial, depending on their purpose because I buy guns to shoot not to "collect" or for investment reasons.
For example: A Stevens single shot target rifle drilled for Unertl scope blocks, or a Springfield sporter with a Griffin&Howe side mount will always capture my attention quicker than a completely unmolested identical rifle. If I were enamored of Savage EG's I would welcome one d/t'ed for scope mounts even if I intended to use it with an aperture sight - A) because that's why God gave us filler screws for when a scope isn't mounted, B) with a cataract just starting in my right eye, a scope is welcome these days (and I won't always have a cataract), and C) because it means I can get it cheaper than the crazy "collector" prices which are the new norm in the world of Savage lever guns. For those reasons I sincerely wish more of them were d/t'ed.
