I've had users complain about these. The margin control seems to have increased in later versions, early on it only locked on to other dimensions, but in NX9 it likes to lock onto the margin distance more. Maybe it's just me, but I've noticed it more in NX9.
I believe these are the prefs you referenced:
As I posted, the defaults for the offsets are there, but is there an on/off toggle for the users that hate it, and don't instinctively go for the alt key? or can they be set to 0 to be "off"?
Setting the value to zero may work (I've not tried that), but since that is in the customer defaults, it will only apply to new parts created with the "blank" template. The option I was referring to is in the dimension dialog (alignment -> position on margin). If you have "dialog memory" enabled, the "position on margin" option will remain off until you re-enable it.