Start with a project set up like this:
Enable Show All Files, and exclude File1.py from the project. Then copy it from Folder to project top-level (either by Ctrl+drag'n'drop, or Ctrl+C / Ctrl+V). The new item will be included in the project.
On the other hand, if you instead exclude File2.py from the project and copy it into Folder, the new item be excluded as well.
Basically, when copying from top-level into a folder, it preserves the inclusion state of the original. But when copying into top-level, it always makes it included.