My peace of mind comes from my self hosting in 2025 looking the same as my self-hosting in 2005 (except a move to systemd). I haven't even re-installed my workstation OS since 2006 or so.
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One change I made that may help with this, is to not install crap on the host that I don't plan to use for a long time. Trying out a new database server or want to set up an Android IDE for a temporary project? Use a VM, don't clutter up random files all over the host. Is this what is happening on your Windows perhaps?
On Arch Linux, all system files are listed, along with their content hashes and expected permissions/ownership, in the installed package database. So it's possible to just list changed files in /etc or unexpected files in the system, or files with unexpected permissions, and do a manual cleanup/checkup if needed. No idea how I'd even approach that on Windows.
I guess the only time I'd need to re-install would be if I messed the system so bad that manual fixup would be too laborious over fresh setup and reconfiguration. (And I'd have to lose system backups too)