> Gemini was also unable to find the .dev, even in "Research Mode."

Unsurprisingly, right? Gemini just uses the same back end as Google itself, which - according to OP - doesn't list his site on page 1, not page 2 and not page 5.

Depending on the prompt, it should have gotten the link from the github, but that's like an indirect hint from a secondary source, it probably ranks the Google index quite highly when it does research.