I've tried editing the Preferences manually, but nothing seems to have any effect on it. (Windows 10)
I found the preferences file here (you'd need to replace "monst" with your user folder name): C:\Users\monst\AppData\Roaming\Opera Software\Opera Stable\Preferences
With Opera shut down I added the .json extension and opened it in Code Editor from the Microsoft Store to Edit > Format Document on it so I could find the extensions > sidebar section more easily. Reordering, saving, then removing the .json extension before reopening Opera. With the Settings sync on it will overwrite the changes, but with it off they'll still change absolutely nothing. I can rearrange them, delete them all, put a dozen copies of the same extension id, or whatever, and the extensions will always show up exactly the same when I reopen Opera without my changes being affected in the file (other than all the formatting being removed).