I think the problem you are experiencing with directly editing the layout like this is rezipping it. I have just tried to do what you would like to without issue, here are the steps I took.
First export the layout, this should create a zip for you. Now open this archive and extract the folder that contains the images or other resources you would like to edit.
You can then directly edit the images from this extracted folder. Once you are done making the edits open up the zip for the layout again and delete the folder you were just working from, then drag back in it's place the folder you had extracted earlier. You can then import the zip file directly.
When I did it like this I was able to replace the folders directly inside of the zip with my updated images being used. When I created a new site from this layout it utilized the images that I updated inside the folders.
