I think it's perfectly reasonable to describe Charles as "non-native".
For example, it doesn't integrate with Keychain, for SSL certificates, so you have to do a bunch of jiggery pokery with the openssl command if you want to generate your own CA for use with SSL interception.
For a more trivial but still annoying example, control-A and control-E don't work in Charles's text fields. In normal Mac apps, this goes to the beginning/end of the line, but in Charles it does nothing.
"Native" isn't about "poor" UI per se, but rather about whether or not it has the basic UI features provided by the system. In a native app, you have to go out of your way to disable stuff like ^A/^E because the system gives that to you by default.
I'm not a purist and will happily use non-native apps like Charles if they get the job done, but it's still a legitimate point against it.