Because on a vessel authorized for only two watches a “12 hour work day” can be assumed to be 12 hours of watch. See the part of the definition of a day in 46 CFR that you cut out if your quote:
46 CFR 10.232
(h) Day. (1) Except as noted otherwise, for the purpose of calculating service in this subchapter, a day is equal to 8 hours of watchstanding or day-working not to include overtime.
If you actually worked two watches, like on a tug, that’s one thing, but just working a twelve hour day doesn’t count.