Why do you think it's less reliable? setTimeout gets clamped by the browser to a minimum of 4ms, so you waste a lot of time when all you want is a task boundary.
I tried so many janky different ways that I don't quite remember how to reproduce it, but I found that setTimeout was more likely to always execute once per animationFrame, where using MessageChannel would sometimes execute more than once per frame. I guess the minimum timeout added to setTimeout makes it more likely to not hit twice between paints. The test setup I have now gets pretty clean results.
One final question would be why you have this uid system with attaching and removing event listeners? I think MessageChannels are order preserving, so you can do with a single EventListener that consumes events off a queue, or am I missing something?