It would be great to have an option where every file saved in non native format is automatically saved as an identical open standard format within the same directory. This would do several things:

Get people accustomed to open standards - a lot of people just default to MSO formats without really knowing about our native format. In many cases our native format results in smaller file size which is awesome.

Loss of Data: Because non native formats result in loss of data sometimes - having an auto save to native format essentially guarantees to prevent this

Efficiency: You could accomplish this by double saving every time but this seems tedious

My suggestion is to include it in "General" in the options, something like "create duplicate file when saving in non native format" -- a bit long, but hard to get to the concept in short format. Perhaps "duplicate native format" with a tooltip "when saving native format, save a duplicate native format in same directory"

Also when working on the non native format file, if you save it, it should automatically update the native format file as well.

Another benefit of this is that people could comfortably set the default to MSO without having to worry about loss of data or any other issue that can come up with saving as non native format. 

Lastly including the option up front when someone saves as a non native format in the dialogue that offers a warning would be a nice additional place to offer the option.