Under the admin/settings for the module, there is the following option:

Default value
If checked, shadowbox integration will be checked in the image detail form by default

Does this control the pop-up value under Extras when adding an image? I have this unchecked and when I add images the pop-up option under extras is enabled by default.

If this is not the correct option, perhaps add a default toggle to admin/settings to allow for disabling the popup option.