I have a much more positive take on this than you, but it depends on your starting point. On my particular bike which I've had since new in '93 (Stumpjumper FS hardtail), I was too low and stretched out in the early years. The changes that improve an old bike (raising the front with fork, bringing hands up in cockpit) shorten the reach, so the end result is way better balanced than the original set up. I've basically optimized what the bare vintage geometry frame can do with regards to fit with my body, and the resulting position allows me to be a lot more capable on this bike than it was in the '90s and '00s. Also, the bottom bracket was too low to begin with, and even with the longer fork, sits lower than modern hardtails with more fork travel. I think the bottom bracket height is now perfect for the amount of travel the fork I'm using has (65mm Marzocchi Z2 Bomber). It's a fully capable and fun ride for old school XC trails (what 90% of mountain bikers actually ride vs. the more hardcore that mtbr and pinkbike attracts).
One part that you can absolutely pick and choose is the bar width. I've been browsing the retrobike (UK) forum lately. I can understand the retro builds having narrow bars, but it puzzles me that the "retro mod" builds also have narrow-ish bars. Once I got away from the narrow bars, I kept going up by feel on both the old bike and a 29er hardtail to where my hands wanted to land naturally, and ended up in the sweet spot that modern cross country riders use (surveying a ton of bike checks of World Cup bikes... between 700mm and 760mm). That's a body position that makes you stable on the bike through corners, as well as give you extra leverage compared to narrow bars to hold your line when terrain is torqueing on the front wheel. I see "modern" bar width as the single best upgrade on a vintage mountain bike ridden on trails. There's no reason it has to be matched to a certain stem length on an old bike.
On my '94 Stumpjumper FS, I've gone up about 25-30mm in fork axle to crown, down 20mm in stem length, up 180mm in bar width, up 80-90mm in saddle to bar drop (to about level with saddle, which is perfect for XC with my slightly negative ape index/shorter arms), and forward in saddle about 20-30mm (despite longer fork, with help of switching from setback to straight seatpost).
If I were to get a custom modern hardtail bike (which I'm not, because this old bike is just right for where and how I ride), I'd put the touch points in the exact same position as I have on the '93 bike now, with only geometry changes to lengthen reach/shorten stem, increase seat angle so saddle sits in middle of the rails, and slacken the head tube a degree or so (currently at around 69.5 from 71 original). I wouldn't go super slack as I'd not be after a Kona Honzo type bike, but an XC hardtail.
I realize that making all these changes might not make sense to an old bike. In my case, I had plenty of ~$5 stems and bars to play around with/optimize fit and $8 forks from the local co-op. The result is so good that I've doubled down on tweaking the '93 bike rather than replace my much more recent 29er XC hardtail (carbon XX1 cranks, 1x11 XT, XT discs, carbon Roval wheels, carbon bars) that was stolen last year.
At this point, because of my style of riding, I don't want anything more. I'm out to enjoy nature with my dog(s), ride for fitness and fun, ride tech uphills, play/practice wheelies and manuals, etc, but not ride increasingly gnarly downhills.