Based on what the navi say we should pasken like the Magen Avraham that day starts at halot hashahar and ends at tzeit. Why we pasken like the Gaon
Salomon Amar, DMD, Ph.D.
This is definitely one of the big proofs brought by those who do not Pasken like the Vilna Gaon (it is the second proof brought by the Minchas Kohen in his first Mamar (ch.2).
However, there are many Gemaros which indicate that the position of the Gaon is correct as well, as discussed at length by the Minchas Kohen. To see a refutation of this proof, see Minchas Kohen Mamar Rishon (ch.8) at length. [You have touched on a subject that requires quite a lengthy discussion. Learning the Minchas Kohen is one way to get to the bottom of the Sugya.]
All the best,
Yaakov