A simple question: Using the user-folders differently

Yes, you can create folders inside your Home. The folders there are not terribly special, but the Finder does treat them as such by putting that badge on the folders.

If you have multiple users and want to keep the folders private, you'll need to change the user permissions on the folders you create. When you create a new folder, it inherits the permissions of the enclosing folder. Your Home is set to allow other users to see directly inside so that they can see your Public folder and so the Web server can see into the Sites folder. Because of that, the new folder you create will allow others to see inside of it.

To change the permissions, select the new Folder and Get Info on it. The info window will open and the permissions are at the bottom. The list of permissions will have you as the owner and you will have read/write access. It will also have a group (I think Staff), and Everyone. Select any Groups (icon with two silhouettes) and delete them (- button). For Everyone, set it to No Access. If you are the only user and you don't share out folders over the network, then it isn't likely necessary to change the permissions.

I can't think of a downside of using other folders. The potential downside of not using iPhoto is you won't have the media browser to select photos from. But, that's not a really big deal if you can easily identify your photos in the file structure.