It’s not just the Nach Meyers. The A is sharp on a lot of old flutes and plenty of newer ones as well; most of the Rudall and Rose flutes (and modern flutes based on that model) that I’ve played have an A that’s at least slightly sharp, more noticeably so in the second octave, and you have to flatten it by dropping your chin slightly so you’re blowing down more into the embouchure hole. The Rudalls also have a deliberately flat bottom D that is brought up to tune by raising your head slightly so you’re blowing more across the hole, plus blowing more strongly. The result is a really nice “open” or “free” bottom D; it takes a bit of practice to learn how to do it, but it becomes second nature.
Edited to add: for a bit of history about this, see Rick Wilson’s page here: http://www.oldflutes.com/19C-play.htm and http://www.oldflutes.com/19C-compare.htm
The need to vary your attack on certain notes to bring them in tune was seen as a feature, not a bug, by many people: there’s a great passage on the first page I linked to above about the individual notes on simple-system flutes being like different “vowels” as sung by a singer, thus the flute’s tone changed from note to note, it wasn’t a tabula rasa like a Boehm-system flute. The flute’s own “personality” is imposed on the music – there’s no master-slave relationship between the player and the instrument; the flute asserts itself and the player has to accommodate the flute.
Imagine how boring the uilleann pipes would sound if every note had the same tonal quality. One of the things that makes the pipes great is that individual notes are immediately recognizeable: the bottom D, the E (especially the second-octave e), the C natural, and the back D in particular stand out and have very distinctive tonal qualities, different from any other notes on the chanter. A good piper can listen to the pipes being played and recognize each note for what it is, just based on its sound.
For info on the tuning idiosyncracies of the old English flutes, see http://www.oldflutes.com/english.htm
The key passage there is: “The large-holed English flutes can be very difficult to handle. Intonation is weird. The low d’ is often very flat, while the a’ and b’ are sharp. The e’‘’ and e’''b can be flat. Often bore shrinkage exacerbates the problems, but these symptoms seem to be part of the design. The correct method of blowing can help. They seem to require a tight embouchure with the lips above but close to the outer edge, and like to be played “on the edge”, where notes, especially the lower octave notes, are about to overblow into higher harmonics. Then the tuning seems better, and the tone is wonderfully rich. No other type of flute can sound like this. But to keep this up for long takes a lot of strength. Nicholson could do it, but some of the rest of us have trouble. I do not feel that I play my best on this style of flute, but after demonstrations that include numerous flutes, many listeners will recall and comment favorably on the memorable and distictive sound of the Nicholson flute.”