The bit I am most confused about is that my understanding is that, with fatalsToBrowser the only two ways to get a 500 error is that the script has the wrong permissions or that the script doesn't return valid HTTP headers. As this is an intermittent problem, it is neither of these.
That is a bit of a non-sequitur. There are many ways for a script not to return valid HTTP headers in an intermittent way. The most obvious one is an intermittent restriction of some O/S level resource: open files, available RAM, etc.
But the errors are not written to the Apache error log
They certainly should be. Are you still running on shared hosting? If so, the real error log is unlikely to be accessible to you as it will (in the case of the event or worker MPM) contain data relevant to any and all of the sites on that shared server. Perhaps have a word with your hoster to see if they can at least give you some of the data which is relevant just to your site. Further, you might consider this as yet another reason to make the move to a VM/VPS instead.
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