I've got some untouched guns, and I've got some highly modified guns, and I love them all! I can't even say I'd rather have a bone stock, unchanged gun, as that would eliminate almost every schuetzen style rifle I own, as almost all were modified a little or a lot!
I have to look at each gun and decide if it's what I want, and the price is commensurate with the condition, changes, and collectability. I actually love old guns with period scopes, and own a few, but I take into consideration that most are likely modified after they left the factory. I think those holes hurt the gun's value, but I also feel that if a correct era scope is still in place it offsets the extra holes.
I purchased a Ballard #6 that was gunsmithed long ago, and had a Stevens scope on it, with Pope rings and bases. It also has a .22 Short Winchester 1885 barrel, and numerous other changes. But I was excited to get it, regardless of how far from factory it was, and I still enjoy it.
Sometimes changes add value to a stock gun, but they have to all go together. The quality of the work, all the features added up, and when those modifications were done, help me decide if I like the rifle or not. Most important ( at least to me!) is when the changes were done. I'm not too interested in one that was modified last year, but early last century (or before!) really gets my juices flowing!