Modal extra option "Show only once" has a side-effect of enabling the checkbox for "Don't Show Again" on modal footer. Even though these are similar options and can probably have shared code, they are independently configured and treated, so this should not happen.
The behavior is the same for 4.x and 5.x versions.
This can be mitigated by manually adding a hide class to modal footer if nothing is supposed to be displayed.
Add a modal;
Check Show Modal Footer. Disable the option "Don't Show Again";
On EXTRAS, check "Show modal only once".
Expected: no visible checkbox appear on the modal footer.
Result: visible checkbox with label "1" appear on the modal footer.
Don't manipulate the dont_show_again variable based on getShowModalOnlyOnce(). This would require small logic changes to the preprocess_html.
Active
5.0
Code
I was testing, I have drupal 10. I followed your instructions to replicate the error, but I couldn't.
Everything seems to be correct, can you provide a little more detail of the error? What version of Drupal do you have? or if you have some module/theme that can interfere with the proper functioning of the module?