Handle mask cube consistently throughout plugins

[rosteen]

Follow-up from #3319, which applied the original mask cube (if one was loaded) to spectral extraction. We should also make sure this is handled consistently in Aperture Photometry, Moment Maps, Collapse, etc.

There was also discussion there that the user should perhaps have the option of whether or not to apply the original mask cube, probably via a menu in the plugin. Deciding what the default should be and implementing that menu is also part of closing this issue.