If it is a restoration, I would want it done how ever it was done in the first place.
I have cues from the 60's and 70's that were done both ways.
I think you mean that newly produced cues generally have the hole drilled.
Cue makers still do it the other way though, I have seen it.
I guess it's personal preference, and availability of materials. For example, if I was doing a restoration on a second calendar Palmer, and the original wrap isn't available (which, it isn't.), I would not regard the wrapping technique as sacred. It's a good example; the second catalog Palmer advertised irish linen wraps that weren't at all; they were dacron, or a dacron-like material. No knock on them, I still have an original with in, and I like it. But no way is it linen, and if restoring it with a change in wrap, I would go for fit and finish with the hole method of installing the linen.
Another example might be an old Rambow. They had real gnarly feeling wraps, because Herman really didn't finish and polish the wrap after he put it on. If I want to play the cue, I would do it the way I want, which would be to finish the wrap smoother.
Again, to each his own. I would say though, that I don't think you'll see a high-end custom cue from Searing, Hercek, Tascarella, Manzino, or a host of others, with the bulge in the linen from the overlay method. Just my opinion. At least I've never seen it. For me, it's fit and finish, unless there's a very good reason to duplicate an older, and possibly cruder looking method.
By the way, speaking of originality, there aren't too many these days that do the old lacquer finish to duplicate the original. Those that do use a more modern lacquer, that in no way resembles the older lacquer of the 60s and 70s. Keeping a restoration really original is highly debatable.
All the best,
WW