Identifying /3/ Program from File

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I have been doing a lot of thinking about how software companies like Autodesk prove that someone has been using a pirated copy of their programs recently, because reasons. Other than the phone home and activation stuff in most of these programs, how do companies know? I'd assume other than hose two methods and reports, they'd have to rely on metadata in the files.

How can a regular user get a look at this metadata, beyond just opening the file in a text editor? Is there any sort of algorithm for encoding vertices in a specific pattern to identify the program that originates a file, or a way the software companies use to determine that from how a file is written or formatted or anything like that?

If you import a file into something like Blender or Open3mod, save it in the native format of said program, and then export from that program, does that remove any metadata or formatting clues that would identify the original program of origin?