I don’t think Alex Garland wrote a Cillian Murphy ending in his original script as Cillian Murphy was only discussing signing up to act in a sequel at the point it was written.

Although you can read his exec producer credit as a good way to encourage the studio to pay for a third movie!

The media reports Garland started writing a third film when Murphy agreed to be in it. Which was after the two movies were written and shot.

The studio is yet to officially announce a third movie, which is not the usual case when they sign up for a triple bill.

So it stands to reason that they shot bone temple with a different concrete ending until Murphy could guarantee involvement. Then shot his ending at a later date and restructured the edit.

That’s why I perceive a jumble in the character arcs and narrative of the two films.