There is a footnote in the book by Dodson and Hilton that James Allen of the Metropolitan Museum of Art gave evidence as to the gender of Neferneferuaten during a presentation in April of 2004 (so quite recent).
Examinations of Neferneferuaten's objects reused in Tutankhamen's tomb show that this individual used the epithet "effective for her husband".
This shows that Neferneferuaten and Smenkhare are not
the same person as some have conjectured.
Theoretically it is still possible that this lady is someone other than Nefertiti, but Neferneferuaten was part of Nefertiti's name...
I wonder if this is the part of the puzzle that has added just enough to the picture that scholars now see enough evidence to conclude that Neferneferuaten-Nefertiti really did become co-regent and may have even ruled on her own?
There is the inscription of Pewah in TT139 which refers to year 3 of Pharaoh Ankh-kheperure and refers to this pharaoh as Neferneferuaten. This shows this is not Smenkhare, but the female Pharaoh then. This inscription indicates Neferneferuaten used an independent dating system. It is not known if her year 1 would line up with year 14 or year 17 of Akhenaten.
TT226 the tomb of the royal tuor Heqareshu is interesting. I have seen people comment on the fact that one of the names mentioned is close to Ankheperure possibly then showing a young prince Smenkhare? (Like Chiaraal mentioned) But I think the names in that scene may be hard to read?
And the problem is also that "--kheperure" names were not that uncommon during that period. So it could just be some other prince