Good topic for debate
Good questions and I am sure that you will get a wide range of answers.
My response to all of your questions would be - it depends.
Depends on what you have and where you are.
In the Uk for as long as firearms have been around, it has been quite acceptable to have a firearm refinished just as you would have your car repainted. I'm talking about some high end sporting arms here.
In North America, there seems to be this fixation of collecting mint condition or as close to mint as possible. Yes very nice, but is like looking for a holy grail at times. Talk to a hardcore Garrand collector and you will understand.
With myself, I am into collecting older military arms, focusing on British and Commonwealth. Yes, I do have a couple of minty rifles that have obviously sat in a rack for most of their life, and I have some that look like they have been used as a cricket bat!
I got into milsurps as it used to be an affordable hobby. Every pay day I would be at the gun shop to brouse the surplus rifles, many complete with bayonet. Out the door with ammo for under a hundred bucks. That wasn't too many years ago either. I tried to buy one of everything and accumalated a pile of them. I shot all of them, used a few for hunting and eventualy settled down and focused on my favourites, the Lee Enfields.
These milsurps were often arsenal refinished and were in pretty good shape. The refinishing was part of their military service life, so some would consider that to be original, some would not.
As for effecting value, consider this example. I had a $60 beater of a Carcano carbine with rust and faded metal finish, beat wood and a bent sight. I replaced the sight, sanded the wood smooth and reblued the metal. The thing now looks pretty. Is this now worth only $30? I think not, probably worth big bucks now, maybe as much as $100.
Another example (theoretical). A vintage Holland and Holland side by side shotgun circa 1900. Faded finish and flaking shellac on the stock. I reblue the metal with cold blue from Cambodian Tire and sand the stock smooth and varnish it. Value before I refinished about $5000, value after about $2000.
Now, if had shipped it back over to HH in England and had them refinish it, value would be up around $10000.
So it depends on what you have to start with. My general rule is; shooter or collector. If a rifle is for shooting then form follows function. It is a tool to get a job done. Paint the frinking thing pink if you think it will help you bag a deer. With a shooter I have no hesitation in changing sights, stocks or whatever it needs. A collectable rifle is different.
With the old rifles that I find at country auctions, pawn shops, gun stores, newspaper classifieds, most are pretty beat. In fact at gunshows, I notice my buddies are attraqcted to the pretty rifles whereas I look at the old beaters covered in military inspector stamps. I can read a rifle like a book and tell you a story about where it has been and perhaps who used it and what action it might have seen. These are the ones that hold interest to me, not the safe queens.
So with new to me rifles, the ones that are complete I basicaly leave well alone. I strip and clean them, check for problems and then reassemble. I may change small parts if it would make them function but otherwise I leave them alone. Metal gets cleaned by soaking in varsol to soften the crud then I go at it with a tooth brush. Rust is tackled with the end of a brass cartridge case and then extra fine steel wool and gun oil. faded finish stays that way. Nothing wrong with honest wear in my eyes. The woodwork would also get a gentle cleaning with fine steel wool and linseed oil to freshen it up, but I would leave the patina alone. This would not effect value, in fact it might even increase it a bit as it is now clean and functional.
Bubba'd rifles. Zero collector value. Most are worth more stripped down and each part sold individualy. So I consider anything fair game when working on one. I will change stocks, replace barrels, weld up scope mount holes, refinish metal, might even spray paint it. What I end up with is a parts gun, nothing more. Value? Approaching the value of an original? No where near, but I am happy with it, I have a gun that can often outperform a rifle worth ten time as much.
So my rule of thumb, if it is rare or collectable, clean it leave it alone. At time that can be very difficult to do. Each bump and ding tells a story, so if in doubt, leave it alone that day, put it back on the rack and look at it another time. If it is a sporter, work on it and build what you want. It won't have value as a collectable but would have value to somebody who wants a rifle that shoots well, which is what rifles are supposed to do.
There, that is my tuppence worth. Hope it helps.