Paul, yes you’re right, this has been tossed around, argued about & debated over many times. I’ve also heard the same thing said on the militaria forums when it comes to cleaning patina..YAWN
Personally, and it really is a personal decision. I try to keep things original, to an extent. I’ll replace a rubbed in jewel with an equal style rubbed in jewel, whenever humanly possible. But I think the main point is to have a functional item rather than an original broken piece that may end up as parts or scrap. But there is also doing any job the right way, or the wrong way as in your punch guy.
I think that you can make a perfectly good, modern repair and do it correctly. Like everything we do is a modern repair, we don’t use antique brass to make bushings, I didn’t use antique brass to make my jewel setting, I used modern stuff but turned it like an original. It looks good and more importantly is works.
My clock, for example, was apparently sitting in an attic for the past 50 yrs. IF I hadn’t been interested in restoring it and had purchased this to use, AND it arrived as it did, the options would be…
1. return it. The seller would probably toss it, value = zero
2. Claim the insurance and try to get someone to repair it, which would be in the region of 500 euros + which personally I wouldn’t pay.
so value again = zero because I would probably just dump it.
3. either I or the original seller would sell it for parts, which would gain some value, but the clock as an individual object would be gone. So again, value = zero
My outlook is what I can do with it TODAY, with what makes me happy right now, which is to restore and make functional and beautiful that which is scrap, hopefully to retain the originality of the piece mechanically and as esthetically as possible without sacrificing functionality.
If, for example, I cannot find an original blue steel mainspring that was the original equipment of a watch, should I not use a new alloy type in order that it shall run? The same could be said for replacing a balance staff that we make ourselves, it isn’t an original factory replacement. It’s homemade using modern steel. That’s how far this originality issue fever can get carried away.
Point is that this whole thing can become taxing because people get swept away by false nostalgia which is emotional and unrealistic. Oh you shouldn’t polish it, all those years of history in the patina! But I love shiny, that’s what I do 
Unfortunately most buy into that emotional pitfall.
To me glue is glue, the only thing I want is for it to hold and do its job. Do I really care that in 80 yrs from now someone might have a hard time pulling it apart and go on a forum to curse the unknown A-hole that used THEN modern glue which is now 80 yrs old….. NO 😆
I care about getting the thing to run, enjoying doing the restoration in a professional way, so that it doesn’t look like a kid did it, and sitting back with a beer and a cig to listen to the chime/tick. Obviously showing you guys the result 
If I had listened to everyone on the NAWCC that told me not to do this or that or that I was an evil person for doing this… None of the watches that I’d saved from obscurity, the parts man, or just the garbage bin, would not now be enjoying being wound, being carried and shown to interested people, being polished and generally admired by yours truly…
So to answer the question, if a job is done right and well, the materials used are irrelevant.. but that’s just how I feel, works for me but not for everyone, but I’ve never really looked for confirmation, just information, one has to make ones own choice and be happy with it… You can’t please everyone so just please yourself 😆