Your comments

Most of these are done, some stuff has been added in the latest version 2.5. Please make separate requests for the features that are still missing.
In Blender they have a "default" project, the one that is loaded when you click "File->New", you can replace it with your own and every time you make a new project you'll get that one instead.

Will it work better for you? There will still be just one default project, but you can adjust it the way you need.
You probably need the camera aspect parameter at the camera panel at the left. Looks like exactly what you want for me.
We've added a special export template with customized snapshot buttons without javascript.
Both Owlet and Koru can now export to Collada, so you can exchange scenes between the apps. Materials are not yet supported as they are too different, but we're working on that.
You can make it out of the simple box + extruded object for handle, or fold it up in Origami and import to Boxshot. These boxes are way too different to add them as an object. Just make it using simpler shapes.
Can you share a sample file or two with that gaps? Thank you.
Does it help to save your settings as a project? Also do you use standalone or Acrobat version?