I just hit this issue too - is there any chance of getting support in the popup before clearing to add custom flags for the script?
Is it better a select box or a text box?
A dropdown of all the different modules from the linked webpage may be one way to do it, however a free-form field to add an custom flags to the pre-clear script might be another (with a suitable warning) as a dropdown with all of the modules may be too overwhelming and looking through the list it doesn't actually reveal which option is the correct one in most cases.
Additionally, a free-form field allows for any flags to be given manually to the script - saving the pop-up from becoming too unwieldy with lots of options that probably remain at "default".