I do similar things. Everything I run is built on top of LXD or KVM so that it remains compatible across time and is not beholden to anything but the Linux kernel, with disk images backed up at key points of the installation process. All of the build scripts are housed at [1] and then I have a set of machine-specific scripts that leverage those to rebuild any of my virtual systems in a single command with no data loss. Press a button, walk away, and in half an hour I have a pristine system with everything I need installed and my data drive mounted.

Any time I'm working on a machine that was set up non-deterministically, I feel vulnerable...

[1] https://github.com/kstenerud/virtual-builders