Hi permezel, thank you for taking the time to report this bug!
I am sorry for this, as it appears to be quite annoying. However I'm unable to reproduce this issue so far. Would you be able to give us more information :
- Other extensions installed
- Orion version (you can find it in Settings → Help and About (near bottom of the list) → About the app)
In the meantime, you can find the Dark Reader options menu in the Settings menu, as you wouldn't find them in the "Website Settings" menu (see screenshot):

Thank you for your help in making Orion a better browser!