For Windows 11, the location HKCU\Software\Microsoft\Notepad is no longer used to save window size and position for notepad. Exploring and testing do not provide a new registry location for this.
If you run Process Monitor when opening and closing Notepad, you will see values read from a registry key that looks like the following:
Notepad.exe RegQueryValue \REGISTRY\WC\Silo16cb54f5-9094-87ae-d593-50e2dc13f03cuser_sid\Software\Microsoft\Notepad\iWindowPosY SUCCESS Type: REG_DWORD, Length: 4, Data: 669
You will note that the start of the path isn't a commonly seen registry hive such as HKCU, HKLM, etc..
What is \REGISTRY\WC? Well looking under:
You can see the various .dat files that back the possible registry hives, so in the case of Notepad, the .dat files on my computer are under:
Where: The SID value, in this case S-1-5-21-4143797489-525809663-3828285892-1047, is the SID of the account running Notepad.
If you run from a command prompt:
whoami /user you will see the SID for the account running the command prompt.
So to answer your question, the configuration is contained in the .dat files.