My guess is that there were perhaps more wood to remove on the bottom side. Or maybe doing it on the headjoint side would have been too high pitched ?

It has to do with adjusting the octaves, wooden instruments have a wall of at least a couple of mm, which allows "undercutting" (so you can retouch the upper octave without moving the 1st too much, in range of more or less 10-20 cents) With very thin walls -such as pvc or a metal flute- the drilling must be precise, because you have no margin to "undercut" the hole in a specific direction. In this example, if he had cut straight on the top side _making the whole hole bigger_ the first low B note (1st octave) would be sharp. Just undercuting on the low side _ without making the hole much bigger - the B note of the 2nd octave goes sharp (like 15-20 cents in this example) But the air pressure has a big impact on accurate intonation, it's part of the technique of the instrument (like in recorders, modern traverse, etc)

@@pedrova8058 thanks for explaining!