If by "embedded" you mean "MMU-less", it's definitely rare these days, even though historically general purpose computers had binary loaders long before they had virtual memory.

NuttX is the only one I can think of off the top of my head with this feature.

> There doesn't seem to be a mainstream embedded OS that allows dynamically loading binaries

I'm not up to date on embedded programming vernacular, but isn't that just a regular OS with apps? (Apple Watch OS, Android Wear, etc)