I understand that, but it's not reasonable to ask that the VM intrusively modify the filesystem without the guest operating system knowing about it: therefore the "correct" solution is some guest userspace utilities for the user to install, which perform these operations from inside the VM. (If a 5 in a file changes to a 6, then rather this change happening from outside the VM, to the total surprise of the guest OS, as though you pulled the hard drive, mounted it in another computer, modified that one value, and remounted it in the original computer, all without the guest OS even being aware that the hard drive had been unmounted or modified, instead, it should be performed by a utility from inside the VM.)

The difference between this proper approach, and what you call "hacks" is minimal, and basically a question of packaging. To be clear, I agree that the VM developer should write and package these utilities for every major guest operating system it supports.