You could use an acf/prepare field filter to remove the layouts that you don’t want to show https://www.advancedcustomfields.com/resources/acfprepare_field/. May be a little complicated. I think you’d need to loop though the layouts in the flex field to find the ones you want to remove. I think that the developer might consider this an “edge” case, but you could try submitting your feature request by opening a new ticket https://support.advancedcustomfields.com/new-ticket/ (the developer really does not read these forums very often)
