Murena are apparently working on some complete backup capability, which is sorely missing when not using TWRP (although TWRP backups aren’t complete by default and TWRP might not be able to decrypt encrypted user data depending on the device), but this should still be months away.
To cover the state of the OS without user data, you can keep OS install files and the tools to install for the OS version you want to backup.
OS install files are here for your device, depending on whether you are running dev or stable …
https://images.ecloud.global/dev/star2lte/
https://images.ecloud.global/stable/star2lte/
You can backup contacts, SMS and call logs via specialised Apps on the phone or via phone syncing tools like MyPhoneExplorer (this one’s Windows only, though).
You can copy “Internal Storage” via USB or possibly via phone syncing tools.
So far, so easy.
“Internal Storage” (the one made visible via USB) is only a part of the data partition holding user data.
So, what’s left out so far is the rest of the data partition, which has the user-installed Apps and their data as well as user settings. By default the user has no access here and is limited to whatever backup or export function all the user-installed Apps provide one by one.
And you can take notes of your settings.
And you can backup APK files of the installed Apps (for reinstalling the Apps more quickly than via a store) with tools like SAI (it’s important that the tools support so-called “split APKs”).
However, /e/OS allows you to enable “Rooted debugging” in the Developer options (once you made them available), and with this you can use adb root to give root to ADB. This gives you access to the rest of the data partition via ADB, so you could try to copy those parts from the phone via ADB, or there are also tools which can use this, example … Android Backup and Restore Tools (ABRT).