Well, that's my point: Being able to use phone apps and desktop apps in parallel.
A priori, there is no technical disadvantage of both environments running at the same time on the same (Android) Linux kernel -- apart from somewhat increased RAM usage which is not really a problem on devices like the Pro1(X) that simply have enough of that.
It is true that Chroot or LXC solutions like mine (on Lineage) or @matf's (on Sailfish) do not have direct hardware access to a lot of features (telephony, GPU, GPS, ...). However, this is not a technical problem: it is a consequence of the kernel