In answer to your questions:
1. Both options are there by default, so to remove from the options altogether would require some minor code modification on your part.
2. This would also require customization as there is no option to disable it from the admin dashboard. Our themes are not encrypted, so you are free to make modifications if you wish.
3. It's not a bug, it's how things are supposed to work. It's all about incentives, you can find more about credit plans on the
theme information page.
4. Not via the admin dashboard, but email content can be changed in the core theme files through customization.
5. The "charge for projects" setting is what tells the theme to redirect the user to PayPal once the listing is being posted, you'll still need this even if the listing is free if you want to still charge for it being featured.
6. Yes all listings are posted on the homepage, with newest at the top. Seeing it twice would become less of an issue once you have more listings. You can control the number of regular listings per page from within the admin but it can't be zero, unless modified.
7. All categories and subcategories are set up by you, so yes you can choose not to use them if you wish.
8. Yes, through modification.
9. Not sure what you mean by this? In particular, you can't log out of the AppThemes demo site, so it's not clear how you saw this occur? Thanks.