Extended tone-hole are just one of the many possibilities to solve voicing issues and to alter the intonation.
Tuning an instrument is unique for each individual making it not an optimization but customization process. There is hardly anything more misunderstood than intonation on woodwind instruments.
Intonation discrepancies are the result of the difference in tone height from one player to another. It is very important that you can easily tune with others.
A well-tuned piano can't be played out of tune, because the player has no influence on the intonation. This is very different for woodwinds. Reeds, mouthpieces, barrels, playing styles, airspeed, playing habits, and many other factors have a huge influence on your intonation.
For example, a traditional jazz, klezmer or folk-musician will play with a loose embouchure and an open mouthpiece. In this case, the player will need a shorter barrel to play in tune. A classical player will play with harder reeds, a more closed mouthpiece tip opening, and higher airspeed.
These are totally different characteristics that need very different customizations. The manufacturer doesn't know where or who will use the instrument. He will have to decide how to tune the instrument and that will depend on the technician in the workshop. He will do it as well as possible but each player will need slight differences based on how they play, the players' accessories (mouthpiece, ligature, reeds, etc.), and the players' sound concept.
Another reason could be, that the player played on an instrument with intonation issues. The musician had to learn to adjust the embouchure to compensate. After a while it becomes second nature and the musician does not notice it anymore. When the player then switches to an instrument which does it correctly from the beginning, chances are very high that the player will over tune these two notes. The possibilities for intonation issues are numerous, but once properly identified, they can be taken care of.
At Lohff & Pfeiffer, we have over 38 years of experience tuning woodwind instruments to the individual needs of every musician. We have surprised players over and over again with our intonation work.