In fairness, there's actually very little difference. My friends luthier did a test to check if maple boards are brighter. But there was no difference according to him.
I am surprised at this, because I can hear a difference with my strats. It may also be the woods as you say, but my 57 is brighter then the 60, the 60 has more mid range push though. I also have a hardtail with a Hank Marvin maple neck and a fake strat which has a copy of my 60 neck, but with an ebony fingerboard and a basswood body. The hardtail is the brightest (but the neck is huge!). The 60 is the most mellow. You can hear this accoustically too. I have had lots of different pickups on them through the years, but the current line up is:
57 Apaches - brilliant sound - hard to put down!
60 Original 60's strat pickup, one has been rewound by Tim because it had started to fray and had shorted out. This was my favourite sounding strat until I got the Apaches
Hardail - Evans single coils - waiting for a set of BK's. I tried the Irish Tours, but they were too bright in this (they are in a custom semi-hollow strat, where they sound great) - I am thinking of Mothers Milks or a custom set.
fake 60 Nailbomb/Trilogy set - this is my 80's sound guitar. I used to have EMG's in it, but the BK's are so much better sounding.
I know that to do this properly I should keep the same pickups, but I have talked with Tim and picked the best sounding pickups for each guitar.