At least on Android you can generate a fake VPN-esque connection locally that passes everything through a proxy, so the proxy isn't exposed to the application
Sure but then the verification will fail since you won't be able to sign the handshake with the "pin'd" cert. (Assuming they implement TLS or other crypto in their own code.) If you aren't modifying the execution environment then it's possible for an app to be "safe".
You already proved that you have access to it. Why is that no question asked?
Normal DV certs are either "add a CNAME, upload a uniquely named html / txt file, or click a link in an email" -- you've already done one of those (automatically in caddy)
There's a big difference between a 10 year-old OS and a two-year old phone, though. Especially if the unlocked model of the phone has received a Marshmallow update, but your carrier decides they don't feel like going through the cert process for that when they could easily twist your arm to getting a nice, new $750 phone instead.
Probably cross-domain abuse. I'd imagine there's a few edge cases that result in behavior Google doesn't want for ads. For example, double serving, accidental clicks, ad obscuring, etc.
Their FAQ does mention that they'll grant exceptions though.