I'm using the script for two missions in Scroll of Atankharzim so far, and I will almost certainly use it for more. One of these missions has two checkpoints and would have been quite intractable to playtest without the script.
Your proposed changes sound good. They are not, strictly speaking, needed, since the script is very satisfactory already (especially now that you've fixed the variable saving). But they would definitely be appreciated and would improve the ease-of-use of the script for future missions.
The deferred file writing would be welcome. The complicated Scroll mission I mentioned has a noticeable freeze for about a half-second when a large checkpoint, involving lots of variables and ships, is saved.
I don't think you would need to worry about backwards compatibility. Just create a new script with a new filename, and make sure that all the function calls are different from the old ones. To make this obvious, you could use e.g. saveship2 rather than the original saveship. You should not need to worry about the savefile format because presumably only newly released missions would use the new savefile.