I'm going to trust uBlock Origin because it is free open source software and I can see everything they are doing with my data. Apple on the other hand forbids reverse engineering safari (trying to understand what it does and how it works).
Once you're a part of the apple eco-system apple could theoretically (and to be clear we're talking about purely theoretical privacy risks in all cases) access your browsing history and also tie that directly to your name, address, credit card/bank account, GPS coordinates, etc.
Putting your privacy in the hands of a company that has so much of your data already is naturally more risky than compartmentalizing. If hackers somehow compromise my browser extension they get access to my browsing history on one device until I notice and correct the problem. If a hacker somehow compromises Apple they could get access to much much more. For all their care and resources Apple is not immune from attacks either. Safari has had a ton of vulnerabilities exposed just this year so far.
Downloading a sketchy browser extension takes deliberate action on the part of the user. Just loading CNN.com can (and has) caused computers to become infected automatically because of ads. Limiting the ability to block ads is not protecting anyone.
Besides, in the end, it's all about minimization of threats. The existence of one threat is better than the existence of two. Don't let perfection be the enemy of the "good enough."