I don't see why your first option would not be ok. You can setup an IWP specific privilege set in your code file that restricts any possible connection to only the IWP layouts, and even the scripts.
You'll want to make sure that the matching users have restricted access in your data file as well if there are special restrictions in your data for IWP connections.
Just remember to thoroughly test your IWP deployment. I'm not as familiar with it as CWP which I primarily use, but if I recall, all should be ok without having to create an entirely separate file.
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Another reason worth considering for adding a fourth file to your deployment is for organizational purposes. Users accessing via IWP and users accessing via FileMaker client software usually have use cases so different that they are worth thinking of as separate apps that happen to use the same data. By keeping them in separate files, you don't have to worry about any IWP concerns when working on your internal application, and vice versa.
thank you mike, for you continued support !!!
Very much appreciated !