Can the machine readable files for integrated circuits be verified by the manufacturer design team?
Can you check if a file is the same over time and location?
Yes. It's called check-sum. 

Can you use the instruction format in the files to check?
If the format is deterministic, of course you can. Just generate the instructions again and check if they are the same.

Do you want to make your own tools for that?
Sure as hell hope not. MD5 is a file-to-file check-sum that is very popular and works on anything, with a pretty high confidence in every bit being the exact same. There are many more. You can even just use a Version Management tool's diff view to compare files and their content and see WHAT changed exactly. An example of a decent diff engine without needing version management suites (but why not get one anyway?) would be WinMerge for Windows.