My preference is to leave things the way I got them. I may switch horns etcetera for awhile when they are on display but when it comes time to sell I'll usually put the machine back in the configuration I found it. I don't think there's anything wrong with for example upgrading to a cleaner case if you have a machine with a nice bedplate and poor case for example but normally I wouldn't do it. If I found something obviously incorrect, A model Triumph case with E model works or something like that, I might try to switch it back.
I would not put two/four minute gearing on a two minute machine or drill holes for a cygnet in a case that did not already have them. If I wanted one in that configuration, I'd just wait for a nice one to come along in the configuration I wanted. If others decide differently, I don't think it's a huge sin though, except drilling the holes
Of course I'd not do anything that's historically incorrect and where there are serial numbers, especially matching serial numbers on case & mechanism for example I think it's a mistake to switch them and the owner is probably reducing the value of the machine should he decide to sell.