By having one. You can make a new project and DEFINE what folders it makes use of. The default just makes sane stuff if you dont have any projects defined. On the other hand if you have some additional stuff loaded they may overrode you. On the other hand if you happen to keep deleting the maya prefs folder then yes maya will keep doing this forever.
Is it possible to just create project files when creating a project?
yes click on the square next to the menu item for options and delete all the folder entries for the types. But in reality no not really your bound to have some folders, or youll just get spammed to death. The point of defining folders for maya is so that maya automatically searches for stuff in/relative to those folders making your files more portable. (otherwise maya will store EVERYTHING as absolute)
So define maya project root (can be anywhere but not in the root of a drive in windows it MUST be a sub folder*). Then define your project there and set that as your current project. Then delete the defaults. Now when maya starts it uses that last current project. (for you other users will default unless a project is set in their prefs)
*But yes you need to have a project no matter what, no way around this. Also you can NEVER have the project root located in the root of a drive no matter how much you try (because doing so would make it impossible to use maya projects on other operating systems). Also maya pretty much requires you to have everything in the project under project root (this is sane because how else do you archive said project)
PS: try not to be too creative on this account. Because it might end up biting you backside really badly. See if you define projects that collect data all over the place and have no clearly defined root folder then you can not transfer the project to others. And you can easily break a maya file by killing some of its dependents.