FULLY agreed!From a software developer's viewpoint, this is our worst nightmare. I would strongly recommend against this approach in any user (or developer) case! This method of installation leaves so much room for error that it isn't even funny -- from settings and saves to assets and libraries.
If not doing this is what a "clean install" means, then I would recommend for a "clean install" every time. Anything less than is just too chaotic and messy to deal with, and near-impossible to troubleshoot. Software are generally not built to be this resilient. This method goes against design -- against how most software are built and work.
You should always start by newly installing the core software, then adding to it the plugins and mods -- preferably one by one and test-running the software, so you know when things break at which mod/plugin it happens, and which combination of additions is responsible for causing the mess (as there are often some mods that don't work well together).
I found the best way is to make an archive of the original game without mods.
Or at least, put those unmodified files on an external HD.
Then next time you want to install, use that archive/HD instead as clean slate.
That works much faster than doing that 2-CD installation process.