I have not seen these proposals, but it does make sense from the perspective of causing the least disruption. The work to sink the tunnel to 145 Street disrupts only the ’s remaining two stations. The can continue running uninterrupted for the most part while the construction is ongoing with the final disruption being to shut down service for connecting the tracks at the new junction.
On the other hand, if the southbound tunnel from the Bronx had to be sunk, then both the and would be disrupted. The would be disrupted by the Harlem River, and both would be disrupted again when the junction finally gets connected.