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Even though I don't recommend relying on it (because it is not very effective), I know quite a few people who only use Google Play Protect.

  1. Does Google Play Protect only scan apps installed via the Google Play Store or does it scan all installed apps?
  2. Does it scan APK files on the device that are not installed?
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From experience

Does Google Play Protect only scan apps installed via the Google Play Store or does it scan all installed apps?

It checks for all apps installed on the device irrespective of source (barring systemless installs using Magisk). For instance V4A (Viper for Android) flashed through TWRP triggered this warning

Does it scan APK files on the device that are not installed?

No, it does not scan APKs. I was transferring APKs of old versions of apps which I prefer over current version and inadvertently copied Lucky Patcher APK. Since I didn't install it, it passed checks

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    +1. I agree too. And I want to add that Google Play Protect actually sucks in what it does. I have URet patcher installed too (an alternative to Lucky Patcher in few cases) and Google Play doesn't detect it as a harmful app.
    – Firelord ♦
    Commented Aug 22, 2018 at 10:18
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    @Firelord Even worse, it doesn't detect Lucky Patcher (vanilla!) on my OnePlus 5/6 in more than half a year.
    – iBug
    Commented Aug 23, 2018 at 5:38

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