@Mario Karp, Thanks for posting in Q&A. To apply the app protection policy separately for iPhone and iPad. We can create different filter in Intune by set the model for iPhone and iPad. (Based as I know, the model for iPad and iPhone is different.)
https://learn.microsoft.com/en-us/mem/intune/fundamentals/filters
After we create the filters, we can add different filter under app protection policy assignment to separate iPhone and iPad.
Hope the above information can help.
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