I guess that's the way it works.
If you'll notice your encoding in AME, it normally maxes out all your CPU cores. It does mine. This is awesome!
But, if you want to edit, you need those cores, especially with Long-GOP footage that relies on CPU for real-time decompression. So, in effect, you're telling your computer to let Pr take over the CPU when you start editing in Pr.
It's a pretty smart way that Adobe enabled this behavior, if you ask me.
It depends on your system. I am working on different systems in different locations, and some of them just go on chugging along. Some of them (those just above the minimum specs) do indeed pause the AME