IMHO more options in an IDE are usually good, if the defaults are ok. I think putting the project files inside the project folder might be a reasonable default at least.

Regarding the naming of Project>New From Folder..., just in case it was missed as I pointed out above this could make people think if a project folder already exists (e.g. cloned from VCS/a repo with geany project files already inside) that it wouldn't work, which would be a bit unlike other IDEs with this concept where you can just pick a folder and if it's empty it creates a project, otherwise it just opens it. That is why I think a more neutral Project>From Folder... might be nice, since then it could adopt this "create or open" concept in its behavior as well.

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