You can just skip the app store, can't you?
I don't have a single store-installed app on my mac and I only get warnings (once) from 1-2 open source apps whose developers don't code-sign.
Neither do apps distributed directly by third parties as long as they are signed etc. (you just need the $100/300 per year apple dev. account for that).
You can just skip the app store, can't you?