I started to post this response in another thread, but decided it would be more appropriate under Repair and Maintenance - Saxophones
Lower Stack Regulation
Regulating the lower stack of a saxophone involves adjusting the feet of the F, E, and (sometimes) D keys in such a way as to contact the backbar of the F# and close it (and the G# and Bis) at the same time. Once this regulation takes place, the cork or other material at the bottom of the feet of the F, E, and D keys is added to or sanded so that there is no "lost motion" before the foot of each key touches the backbar of the F#. This process, which is the correct way to regulate a saxophone's lower stack automatically results in the keys being in the same plane when open just as they were designed to be at the factory.
Key Height, Venting, and Intonation
The key height of the stack is normally adjusted so that the most under-vented notes speak clearly. Under-vented notes are those that vent through an open tonehole followed by a closed tonehole. Some of these are called "crossfingerings". The under-vented notes on the lower stack are F# venting through the F tonehole followed by the closed tonehole E, and E venting through the D tonehole followed by the closed tonehole Eb. This height is determined by the timbre (clarity) of the note, not by its intonation. If a fully vented note is uncomfortably sharp, putting a "crescent" in the upstream side of its venting tonehole can solve the intonation problem without making the note stuffy or introducing lost motion. If a fully vented note is flat is the topic of another even longer dissertation.
Over and Under Venting
It is true that some players prefer the key openings to be higher than they need to be for more more volume and projection. The tradeoff, of course, is increased key movement which can affect technique. The rule of thumb is that once the key is raised approximately 1/3 of the tonehole's diameter, raising it higher has no additional effect upon the pitch or timbre of the note. Some vintage saxes seem to work best with lower key heights compensated for by pushing the mouthpiece farther onto the cork.
Upper Stack Regulation
The upper stack is regulated and adjusted using the same principles stated above, except is the small C key that is closed by the B and A keys, and the under-vented notes are the C and A. The only way to adjust a sax setting the key height of each key independently of the others as suggested in the quote above would create "lost motion" in the keyboard that would not be acceptable to players of even modest ability.