You may be aware that it is now a lot more difficult -- if not impossible -- to modify the OS installation itself, as it is now on a Signed Secure, read-only Volume. Modifying the OS volume can lead to it refusing to boot.
The OS and "everything you install or change" are now completely separate, which eliminates the need to reinstall the OS for most reasons, and makes it easy to restore your user content, if necessary.
Changing the version of python will not have "modified the OS": you just installed an additional python. Installing stuff with homebrew will also not have modified the OS: you just added homebrew stuff. Files in
/etc are not part of the system volume, as they are largely configuration files and changeable content. None of that needs SIP disabled.
Unless you made major modifications to the OS itself after you installed the last update of Monterey (e.g. booted into Recovery, mounting the System as writable, and modified files in
/bin, rather than just installing additional stuff or changing files in
/etc), then you should just be able to update the OS, and you will still have your additional components.
If you want 'a list of everything you've installed or modified': then there isn't one, short of the complete file listing of the Data volume.