Because it blurs the line between a web page and the browser chrome. Any web page that attempts to look like the browser should be considered malware.

Because you associate it with an error that you have no control over? I find that I'm tuned to recognise patterns of behaviour, so when the patterns look similar to other things, but aren't the same, it's quite confusing.

It is literally training users to dismiss these kind of errors. In Chrome, these errors are really bad, like a safebrowsing warning or a TLS error.

On the other hand, this warning will probably happen a lot! Is Google going to be able to "validate" apps fast enough?

G-Suite and Chrome are different products, so yes, It's perfectly reasonable to expect them to be separate.