[freedumb2003]

Definitions matter. "Methodological materialism" in your context changes to fit each new discovery, so discoveries like the Big Bang and the catastrophic formation of the Channeled Scablands which were derided in scientific circles because of their tangential support of Biblical accounts don't satisfy your question. But at the time, they did indeed require abandoning what were considered at the time to be "methodological materialism" for a seemingly religious explanation. After which, the definition of methodological naturalism expanded to account for each.

In which of your examples was "methodological naturalism" expanded to include an intelligent designer or the direct hand of the Creator?

[dan1123]

In which of your examples was "methodological naturalism" expanded to include an intelligent designer or the direct hand of the Creator?

It doesn't matter. Just like Intelligent Design states, you don't need to define or even include God--you just need to describe the designer's actions. This is apparently enough for you to reject the hypothesis out of hand, just as it was for the steady-state universe adherents when the Big Bang was first proposed and the uniformitarianists when J Harlen Bretz first postulated how the Channeled Scablands were formed.