Please note that these thoughts are entirely based on my personal experience reviewing WordPress themes and are not officially endorsed by Envato. Following these guidelines does not guarantee an approval – though you will probably have a much quicker time getting there!
Regarding including plugins using TGMPA, the theme check does not allow plugins to be bundled within the theme. How would you recommend including pre-packaged plugins? I’ve been including them within the download package, but then TGMPA cannot find and install it. I’ve also used an external URL which works well but is not always reliable. Just wondering if there was a good way I’m not aware of?
Unfortunately that happens sometimes, but we have been working on improving the process. From a reviewer’s standpoint it’s tough to identify every issue, every time. I suggest checking for PHP notices/warnings, doubling up on the suggestions in my article, and refine your item. You wouldn’t want a theme with errors approved in the first place anyhow.
Regarding your .pot question: The localization file should be in English and delivered as a {theme-slug}.pot file that contains all your translation strings. Theme can include an actual translation files, but it should not add the en_US.mo or en_US.po because English is implied.