Yatish
I might have figured out the confusion.
Point 1: Offering of Viśeṣārghya.
It’s been established that the tarpaṇa is performed with 2nd M [i.e. meat].
To bolster this point, in the Parā Krama of Parasurama Kalpa Sutra (8.16) we find the description of the Goddess of Nectar (Sudhā Devi) which says that she holds in her two hands a pot of nectar and a piece of meat.
Point 2: Substitute for the 2nd M
As you pointed out, Nityotsava, quoting multiple sources, lays out some of the substitutes for the:
- 2nd M [i.e. meat]: radish; banana; and
- 3rd M [i.e. fish]: salt; fresh ginger; oil cakes; dry ginger; wheat; māṣa beans and garlic.
Per PKS both of these have to be present in the viśeṣārghya but only the 2nd M is used for the tarpaṇam.
Bringing it all together:
In our tradition ginger is used to perform the tarpaṇam which automatically makes it a substitute for the 2nd M, even though, as you rightfully pointed out, Nityotsava lists it as one of many substitutes for the 3rd M.