Hi Dev,
I cant think of a way where you can do both simultaneously, so I think you either have to compromise on forcing the filter at the folder level and train the users to drag and drop into query filters when they want to use prompt, while still having the flexibility of creating custom query filters with constant values etc on the base object.
Or you go with forcing the prompt and make it as optional and ask them to use it for any query restrictions associated with it as prompts, else they can leave prompt unanswered and create the query filter on base object to perform their constant value filtering.
Thanks
Mallik