I’ll just chip in to say the “big reason” when Media Encoder was introduced was that it enabled you to keep working in After Effects while rendering. And you could also do cute things like set up a render farm for a shared drive really very easily. (I did that at the school I used to work with and it was so convenient.)
I continue to use AME because I’ve got used to doing it that way and I have all the presets there. While Render Queue does have MP4, last time I looked there weren’t as many options, so I stuck with my current workflow. AME added notifications before AE did too, so it feels like Adobe consider it the go-to method with features being later added to After Effects.
The final reason I continue to use Media Encoder is that more often than not, I’m rendering overnight. So I can stack up several renders from different projects more easily.
In summary: it’s what I’m used to, I like not having to lock up AE while rendering BUT if it’s not right for you then there’s no need to force yourself to use it.