The Yerushalmi (Ta'anis beg 4th perek) cites as proof to R' Yochanan's opinion that tefilas neilah is said during the day and not, as Rav held, at shkiya, a braysa which says that birchas kohanim is recited during neilah -- since birchas kohanim cannot be recited at night, QED that neilah must also not be said at night. Yet, the Magen Avraham (623:3) quotes a Mahari"l who held l'halacha that even if neilah is delayed until night, birchas kohanim is still recited. At first glance this statement of the Mahari"l is in direct contradiction to the Yerushalmi.
R' Soloveitchik (Shiurim l'Zecher Aba Mori vol2. p. 215) explained that birchas kohanim has a double role of a mitzvah in its own right and an aspect of tefilah. The recitation of birchas kohanim in shmoneh esrei is not just the context in which we fulfill the mitzvah of b"k, but indicates that b"k is itself part and parcel of the mitzvah of tefilah.
The dispute between Rav and R' Yochanan was not simply when to recite neilah, but was a dispute as to the character of the neilah prayer: is neilah categorically a tefilah associated with the day, like shacharis and mincha, or is neilah, like ma'ariv, a tefilah associated with night? The Yerushalmi's proves that the categorical nature of neilah is that of a day-prayer because otherwise birchas kohanim would have no basis as part of its text.
Maharil opined that if one begins the neilah tefilah late in the day and it extends into the night, the text of the tefilah as a day-prayer still can contain birchas kohanim because starting late does not change the fundemental character of neilah as a tefilah associated with the day.