Actually, it's beyond just fret count and the extra few notes.
Imagine these two scenarios:
IF two necks were to be built with all things similar except number of frets, the extra fret will have to be accommodated into the neck somehow. Hence, the stretching and fretting of notes and chords will definitely be affected. Also, a fret board with closer frets means there is less contact of the string on the wood of the fretboard, hence the tone and feel will definitely be affected. It's like comparing fretting the lower scales and higher scales of your fretboard.
However, IF the neck length differs to accommodate for the added or lack of frets, then the length of slack between the point of contacts between nut/finger and bridge will be affected as well ie longer necks = more slack = more roundness in the tone.
I do have to say that this won't matter squat when you throw in the pickups, pedals, amp eq and amp itself into the equation