Same as @gadgetman. Its not a rare, collectible or antique firearm so it isn't hurting it. You refinishing the stock on it isn't much different.
Does it miss by miles and need a ton of work or does it just miss?
Just remember 1000's upon 1000's of ex military Mausers and Enfields had far more drastic things done to them in the way of bent/cut reprofiled bolts and magazines etc etc to sporterised them and they look just fine. Sometimes just damn good.
Why worry about rectifying it later at all? Not suggesting you attack it with a 9" grinder but a little judicious filing/polishing and why wouldn't you have a permanent modification that doesn't look out of place and lets you have pick from a wider variety of scopes. Once its done its done. If done properly nothing to rectify
If not ghost around a couple of gunshops that have JW's with scopes fitted and do a bit of spywork on what fits.
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