Double header for skylight frame
Option B is the better choice.

(A) may eliminate some drywall patching, but will not provide the same strength as it  different load forces at work.

Option A will create a pivot point that will be more torsion/twisting force. Each connection wanting to act like a hinge under weight and pull away from their connections, which will take less energy than shearing.

The header spanning across the full space (B) as a single structure is mostly bending (Compression and tension) force against the middle that will be pressed on the connection with outer joists (and some shear force where nailed to joists).

Think about the pressure on your roof will be pushing at least in part down on that middle joist.

See https://www.teachengineering.org/lessons/view/wpi_lesson_1 for an overview of load types.