If the Commission’s main mission was to ensure that the apocalypse came to fruition, this could only be because Founder Five, who created the Commission, realized at some point that the marigold and the family’s birth was the catalyst for the end of the world (maybe he visited the diner). Founder Five created the Commission and set about ensuring the apocalypse in every timeline, the traumatic dystopia that raised him, in order to save the lives of his family.
Founder Five tried his whole life to find his way back to his original family and his original jump, willfully complicit in the annihilation of several worlds along the way. He urges Five not to save the world, in an effort to save their family, but does not tell Five why.
Five’s drive to save the world is rooted in his drive to save his family. He originally sets out to stop the apocalypse in our main timeline so that his family does not die and he does not find them in the rubble. Founder Five’s warning is consistent with the fact that the apocalypse happens because the family lives. For Five to resign and urge his family to sacrifice themselves in order to save the world for the rest of humanity is misaligned with his main character motivation in every iteration of himself and in every timeline. It negates the complex character work, the antihero air to all our characters, and the plot development that led up to the last episode. And honestly, it was just very lazy writing.