No, there's no way to configure it for the module only. I imagine it could be accomplished but it could cause more problems especially on the support end for the site host. I'd be willing to bet that either hosters would get emails or the forums here would have numerous posts from users who set the file limit far higher than what the web.config has in it and the file size set in the web.config would override any setting done at the module level.

I don't have a copy of Visual Studio or the source handy on this computer and I left my laptop at work tonight so I can't answer whether the extension filter can be changed or not. It's a Microsoft control but I'm guessing that any filters that can be set are done in the code behind. I can't remember if that's the case with the Repository or if it's using Microsoft's default filters.

Module Settings: I think you're doing your settings in the wrong area. Under Basic Settings->Permissions you generally only want to check View and only Edit for users you want to have total control over the module. In the scenario you described you want View checked for Registered Users (if all users can view the page but only Registered Users upload then just check All Users). That said, where you want to set the actual Upload permissions is farther down. Click on the + sign beside Repository Settings. That'll expand that section and about 1/2 way through it is where you can set the Download, Upload, Moderation, Comment, and Rating permissions.

Most definitely if you go into the Repository Settings area I mentioned in my post above. Below would be the settings you use.

Moderation Roles: Administrators checked
Download Roles: All Users checked
Upload Roles: Registered Users checked
Rating and Comment Roles: Your choice