As I recall from working at 'Royces in the 70s and 80s, the reference speeds for 100%N1 were nominal figures for the 'fan design point' (TOC) and anyway were rounded off to a convenient number (3900 on -535 and 3600 on -22 and -524 if I remember right). Speeds above 100% may thus be within operating limits in some conditions and may vary between different dash no variants of the same engine.
So I think the answer to the question is that there isn't a strict definition of 100%N1 its just a convenient way of standardising dial presentations.
Anyone care to shoot me down in flames?