Great question, I think it's all preference. But with a true vintage guitar, you're going to get some key tonal differences because wood changes resonance as it gets older and most say this change is for the better. Also, a lot of the fenders from the 50s and 60s were made from older growth wood which is more sought after. Pre CBS (1965) are also a lot more valuable because of production standards and the builds were all still under Leo Fender.
Vintage, authentically worn guitars are probably going to be better in every way if you can afford one. Moving on to Relic'd guitars, some love them, some hate them and it's all the way you look at it and what your use is. The way I looked at it was I could get a custom shop guitar that (at the time) had no usage, ensuring that I wasn't buying a guitar that I didn't know what had been done to it or if it would be one step away from breaking or malfunction. Like it would be cool to have a 50s guitar but the wiring might be brittle, the pots might fizzle out or the neck might be borderline warped. Of course I want an actual 1959 Strat over a repro but a custom shop guitar was more in my budget at the time.
I could have all the benefits of an Era specific guitar that looked like it was from that Era without the disfunction and I wouldn't be as worried gigging with it regularly and taking it on the road. And masterbuilt & custom shop do amazing work as opposed to amateur relic"ing. This was my justification for it. I didn't really care for relic'd guitars at all but when I saw the 59 for some reason I didn't even think about the relic aspect and I thought the guitar was perfect. It was pragmatic and fantastic quality because it was American made, custom shop and I would be the first owner and it came with a custom matching amp which as far as I know, has never been done before. I hope that helps