In regards to your point #3, there is currently a small workaround for that, where you can force a restore point, by simply editing a file, before you execute your prompt.
Save → Press enter at the bottom of a random file → Execute prompt. You now have a new restore point.
Is it optimal? No, but at least you can create them.
You mean adding an empty line in any of the code files to make it possible to save manually? If that’s what you mean, it is a useful (but time consuming) work-around for the time being