If the code is tagged as being MIT in GitHub and includes an MIT license file, can an author reasonably argue that an end-user is receiving the code under a different license?
Maybe. MIT license permits additional license restrictions on top of license. For example, MIT code can be copied into a proprietary system with a different license, which will forbid copying code out.
Yes
> includes an MIT license file
Maybe. MIT license permits additional license restrictions on top of license. For example, MIT code can be copied into a proprietary system with a different license, which will forbid copying code out.