I hope this doesn’t sound like nitpicking, but of course clearing cache/data of an app will at least delete some files on the phone 
Of course it’s better safe than sorry, but I just checked the app info of the two respective apps on my phone. External files uses 110kB and media storage uses 49MB. Clearing those surely doesn’t delete all files on the phone (around 20GB internal and 60GB on sd card).
But use at your own risk