This is really, really nice! To bad I spent so much time making templates, rulers and overlays that are crap compared to what you've put together.
I've found a few bugs that can wait for now, as they might be fixed in the v41 release. For example, when you have:
console_transparent = 1
console_color = 0 (background)
color_selected_bg = 0
The selected background should be transparent, but isn't.
Also some of the coordinates a little bit off visually (I haven't tested to see if it's just in the Configurator and not passed to the loader. Hopefully you'll support 800x480 & 854x480 images without cropping in the future.
Again, great work and thanks!
Did you read the instructions? If you want it to be transparent, just don't click the "draw console" button

. That button is your transparent flag. The tool tip for that button does warn you of that now.
The sizes I was using were a little wrong in the currently released version (they drew one too few pixels), but I'm pretty sure I got it right in the v41 version.
And yes, the new auto-sized images are supported in the new version. It will still display the image in 640x480 resolution, so it will appear squashed, but that is necessary for selecting coordinates.