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Found this on Sheldons website
http://www.sheldonbrown.com/tooltips/cartridge.html
If you scroll down about 1/4 and look at the table you will see that a PW BB is actually 67mm wide so there should definitely not be any thread protruding, provided the BB is centred of course.
This is what I was thinking. Around half the cup can't be right. I've not tried putting the cranks on yet, wanted to get it sorted first but you make a good point.