What exactly is a flatpak runtime? Is it a virtual machine like JVM (Java) and CPython? Or is it more like something like virtualenv? I already read the flatpak documentation but it was not clear to me.
It is more like virtualenv than JVM or the like. It creates an isolated set of files so that one application's dependencies are well-defined.
However, rather than copying all dependencies into this environment, some are shared in a safe way -- this is the "runtime".