How did you do your tests? Did you manually time and check world gen stats? Or did you use cmd line?
Given that the difference between them was so large it isn't a case where human error matters much.
Sat with the button ready, waited to see the clock tick over from :29 to :30, hit enter, waited 3 minutes, hit enter when it clicked over from :29 to :30, noted when it actually stopped, exported sites and pops.
Afterwards I started a run when the clock went from :29 to :30, hit enter when it rolled over to year 297 so it would end on year 300, noted the times involved, exported sites and pops.
On the 32 bit versions I had cases where the population explosions (campsites seem to remove wildlife from the roaming populations without removing the currently present populations so they keep doubling?
http://www.bay12games.com/dwarves/mantisbt/view.php?id=9925 is the bug report) left the entire computer frozen at much less than the total ram available because of df hanging, on the 64 bit versions I was able to max out and use all available ram before everything froze up. It's a pretty significant overhead change which is most noticeable in situations where you would previously be slamming into fps death, now you've got more breathing room.
The most extreme lag I've induced on 64 bit is deconstructing a dark fortress with huge populations of beak dogs and blizzard men while standing in hell, it took over an hour for the collapse to finish in one case.