I have the same problem, and it's very frustrating. Beyond frustrating. I used to rename the default_partners.json file, but as noted by the OP, this no longer works. There is no coding reason behind this. Opera is in business with these companies, and they're willing to force a decision down our throats. We can deal with it, or ditch Opera.
I'm in the exact same boat as most of you. I've had 'y' as my shortcut for YouTube for ages, as well as other shortcuts that are no longer available to me. I've never used Yahoo for anything other than fantasy sports. Seriously. In all the years it's been in existence. Does someone think that locking it in as a default is suddenly going to make me use it?
I started using Opera during my Freshman year of college, sometime in the fall of 1998. I'm coming up on 17 years, and I honestly don't know why anymore. It used to be for very specific reasons. It was fast. Innovative. Had great features. It even used to be my default mail client (remember that?). Now? I'd guess blind loyalty mixed with the human aversion to change. I use in on multiple OSs and my smartphone. Then the bookmarks fiasco, this default search engine BS. Why is a company with -- let's face it -- a small market share craping on people still willing to stick with it? I'm sure there are business reasons that someone is using as justification. And we can use different shortcuts. So if Opera needs DuckDuckGo (whatever the f that is) to stay afloat, I guess we suck it up. And that sucks. Because Opera had a lot to offer. But so does Firefox. Other browsers caught up.
I mean, look at it: https://en.wikipedia.org/wiki/Usage_share_of_web_browsers. When you only have 1-5% of users, you probably do whatever you have to. Even if you annoy that tiny, tiny portion willing to stick with you. Sucks for us.
Just wanted to mention that the extension "modern scroll" can bypass the problem by implementing it's own middle mouse button scrolling. Can even set it to stop at mouse wheel scrolling, like it was in Opera 12.16, which is definitely a plus, too.