The trussrod ends well before the 'guitar portion' of the neck, i.e. at around like 14th fret or so, so it simply cannot affect the 'heel' portion of the neck which will always stay at the same set angle with the body.

Too often it's assumed that the best fretboard is entirely flat too, which is not the case. If I make a best possible fretboard, the frets will be lower than others under the thicker strings in the middle to allow for more clearance for vibration for instance, since they need it. Or in other words, a great neck has an almost perfectly flat shape with very little relief under the highest string but will bend more and have more relief under the low strings.

It depends on the playing style and preferences, but sometimes it may be preferable to for instance to have the least clearance between the frets and the string at the last i.e. 22-24th fret and not the middle of the string (12th) or in the middle of the fretboard /circa 7th fret).

Quite often such small details are what make handmade instruments better than factory ones. Perfect, straight lines aren't the best on a guitar fretboard.