I originally used "src" because when combined with virtualenvwrapper.project you get a "project/src" directory. After using it like that for a while, though, I agree that calling it "project/project" makes it easier to use other tools (especially Murky).
The main source code repository may be only part of the project. I frequently have files that are not in source control (e.g., tarballs of source for dependencies), branch repositories, and other stuff that I want in my project directory but not in the DVCS.
Yeah, that's pretty much what I do. You can give more than one template to mkproject, so if you have another template you can use it to pre-install stuff. For example, if there was a "django" template you could "mkproject -t django -t bitbucket myproject" and have it install Django then check out the source for myproject from bitbucket.