Personally, I wholeheartedly concur with Apple's decision on this point. Consider:
Suppose a very popular browser vendor were to abruptly decide to swap out Webkit in favor of the theoretical "maximal-ad-injection-and-invasive-tracking-and-covert-bitcoin-mining-engine-dujour!" but they only put a very small and vague indicator in their app update log about the change when pushing it out to their existing userbase. Suddenly, tens of thousands* of new bitcoin miners (et al) just came online overnight, and it all happened in the background automatically, thanks to Apple's default auto-update features.
There would of course be an immense uproar among technically savvy users, who would jump into forums like this one to air their grievance, and likely many of those users would stop using that browser... but the people who don't read MacRumors and the like? That change could completely fly under the radar for a large number of those users.
Apple obviously doesn't want that; they want the users who download these alternate browsers with potentially significant differences in behavior to know full well what they're getting into when they click the download button, and -- perhaps more importantly -- to still have a fallback position in the form of the original Webkit version of that browser, in case the new engine turns to be a bad move for some reason. It's a wise move on Apple's part.
* I won't say "millions of users" because... it is, after all, just the EU users.