I am having some trouble getting around the axle so to speak.
We should naturally make it so you can uncheck "Use as folder thumbnail" too, not just allow another thumbnail to be assigned.
If I select (via right click, edit window) "Include Original" for an individual (or more) image(s) it appears that I ALSO have to manually then check "Settings > Pages > Copy originals" to have these selected originals included in any final album.
True. Otherwise Jalbum just adds a link to that original. This way you have the option to only link or to link and include. When would you just want to link you may ask? I'd say, when the original image location is accessible for the web server too.