That's one reason, but not the only reason. Security is another big one in that the WebKit process is running with privileges that Apple does not want to award to any other app process on the platform, much less a third-party one.
They also want to make sure that if they fix the next security flaw what will undoubtedly be reported in WebKit, that all the apps with an embedded browser will get the fix and won't continue to be vulnerable due to them not updating whatever version of Chromium they were embedding.
Of course, between sandboxing and not allowing JIT compilation, those vulnerabilities couldn't do do much harm, but that embedded Chromium also wouldn't be much fun to use.
Which means, if you let me make a prediction of the future, that when Apple is forced into allowing other browser engines, articles will be written about how Apple is complying by the letter of the law but not the spirit by "seriously hampering 3rd party engines" compared to their own by now allowing JIT compilation.
If they had to then also allow those 3rd party engines to do JIT compilation and bypass the sandbox in means that browser engines need to, then we'll be in a much worse position security wise.
We'll see how this is going to play out, but I'm pretty sure exerting control is not the only reason for Apples' stance.