That doesn't make much sense to me...
A) The Seiko
6R15A data sheet states, "Pull out the crown to the second click when the second hand is at the 12 o’clock position.". But, this is for convenience of setting the time & getting the second hand to line up at 12 at the top of the minute, not because the crown / stem / clutch are in some way dependent on the orientation of the seconds hand.
B) The seconds hand itself is not really part of the watch movement, but the seconds pinion is, & the seconds pinion inside the watch movement has no 'awareness' of the orientation of the seconds hand up on the top-side of the dial. The seconds hand could be off pointing in any direction (or be completely absent from the watch), & the seconds pinion would not know or care.
The position/state of the winding stem is dependent on the contours of the detents on the setting lever spring. If the winding stem is having difficulty locating the setting position, then this would be a good place to start looking for for the root cause of the issue.
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