The DIEP and the nipple are unrelated with respect to the success of one or the other in the initial operation. So, it makes more sense for the breast surgical Oncologist to core/sample the nipple contents in the initial operation at the time of the associated mastectomy. I would consider that to be the standard. Re. the issue of the nipple being a "skin graft", it isn't really sensible to regard the nipple as a skin graft any more than the surrounding preserved skin of the breast would be. The preserved nipple has blood supply just as does the surrounding skin.
Therefore, my thinking on the nipple handling is that it makes more sense to core it at the first operation since emptying it can identify any abnormal cells at the time of mastectomy. Secondly, since emptying the nipple can sometimes cause it to collapse some, a graft can be added under the nipple at the second stage to restore its projection should it be necessary.
Re. #2, it takes 2 stages usually. First stage mastectomy, nipple coring, DIEP. Second stage, any aesthetic adjustments necessary.
Hope this helps,