Is there any difference between changing video containers with ffmpeg vs just renaming with windows?
No, a Windows (or Mac or Linux) file rename will not change the container. They are inherently different file formats. They store data differently. They reference the audio and video tracks differently. Re-wrapping from one container to another can actually be a fairly complex operation depending on how the two formats store essence tracks. It may seem like ffmpeg isn't doing any "real work" compared to a transcode, but that is because the video doesn't have to be decoded in a re-wrap. The compressed bits only need to be re-written in a new order with some new metadata.

Think about it this way: just renaming a Word document from .docx to .xlsx doesn't make it an Excel workbook. Your story doesn't get turned into a spreadsheet just because you changed the extension. You need to a use a program to convert every tab into a cell.

The only exception where a simple rename works is where the extensions are synonyms of each other. For example, if you have a program that is expecting all QuickTime wrapped files to be .qt, but you have a .mov, you can rename the file to get it to work. But that is only because they are two different extensions that identify the same container format.