Brave certainly blocks ads by default, I personally don't see a problem with that. Users can't install adblocker addons in browsers, not much different than downloading an adblocking-by-default browser.

I can't immediately find a source for the publisher opt-in thing. But brave definitely hasn't been doing anything like that in 2016 as your articles suggest, because they only just started now with beta testing brave ads[0]. From my personal testing of brave a couple of times, with the ad opt-in activated, I have also never seen this happening.

And publishers (now) seem willing to join[1].

[0] https://techcrunch.com/2018/06/20/blockchain-browser-brave-s...

[1] https://www.cnet.com/news/ad-blocking-brave-browser-gets-dow...