Play Protect blocks malicious apps, not network traffic, so no, it obviously doesn't interfere with Google's apps.

AFAIK it also left SmartTube (an alternative YouTube client) alone until the developer got pwned and the app trojanized with this kind of SDK, and the clean versions are AFAIK again being left alone. No guarantee that it won't change in the future, of course, but so far they seem to not be abusing it.

Does malicious mean interfering with Google's business model, or does it include intrusive advertising?