@sphere, I understand why you don't want to move the location of 5V fan, but if are able to get creative with routing, it may be for the best.
1 in 3 of my SXL2 heatsinks are factory placed off-centre.
1 in 2 of my IBM 5x86c heatsinks are factory placed off-centre.
The clearance values I gave you are for heatsinks placed on centre. They have a thermal pad type of tape under them. To remove and re-secure the heatsink, I think, is not a move most people would be interested in. I wouldn't do it.
If someone buys an SXL2-66 and the heatsink is off-centred, thus cannot get the fan header on without a lot of bending, it can be avoided by putting the fan header on the outside of the overhang. 99% of people probably won't use those two pins from u1 and u2 as the application is very specific. Thus, the user with an off-centred heatsink would simply not solder on that inner header, or if already soldered on, simply cut the leads off. Moving the 5V for fan one position over makes the unit more versatile in this regard. If it simply cannot be done, then so be it. It is far better to have a smaller overhang than moving the header out further.
Here is an factory off-centred heatsink placed next to a factory centred heatsink. The offset shown is 1.0 mm.
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For the on-centred heatsink, with alpha1, I noted previously we had 0.7 mm clearance. If you recall, I said for safe keeping, you can move that header 0.5 mm closer to the CPU. So now we only have 0.2 mm clearance for on-centred heatsinks.
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Now that same heatsink/CPU placed into alpha1:
The attachment Heatsink_off_centre_with_fan_conn.JPG is no longer available
That amount of bend is BEFORE you moved the header 0.5 mm inward. You did this in order to make the overhang smaller. I am proposing that you keep the header and overhang as they are (smaller than alpha1) and just re-route 5V fan to the outer portion of the header. U1/U2 pins on the inside towards the heatsink, and MEMW#, 5V, GND on the outer edge of the overhang. If it cannot be done, or you don't want to deal with it any longer, that's perfectly understandable. Keep in mind that the 5V fan is only 80 mA. Will the re-routed traces be too narrow to handle that?
In general, if someone is going to use a 5V peltier and some massive heatsink/fan combination, they are better off running it directly from the molex, not the replica's header.
EDIT: In summary, I am weighing probabilities. The probability that someone is going to use u1/u2 AND has an off-centred heatsink is far lower than the user not using u1/u2 who has an off-centred heatsink.
Plan your life wisely, you'll be dead before you know it.