My searches of this forum show me that there has been plenty of discussion about Pixelmator opening and saving in Pixelmator format. I'm sure that this has been a continuing pain the rectal aperture for you guys, but here we go again!
On input, you're doing it right; when the user launches a document, Pixelmator figures out the format and opens it correctly. It will even go so far as to save in the format in which it was opened. Right on!
However, on output, Pixelmator has the irritating habit of really trying to get the user to save it in Pixelmator format. I see from old discussions that this was the preference of many users. But I think that there's an easier way.
I remember many years ago that a popular graphics application -- possibly even Pixelmator -- that had a nice way to handle output formats. There was a preferences option that allowed you to save in any format you specified. You could still use the pop-up menu in the file save dialog box to select a format different from your usual. The current system forces you to accept Pixelmator as the default output format.
For me, this is a pain, as I frequently want to output my files in an Internet-compatible format -- usually JPG or PNG. Whenever I want to save a file, I must click on the checkbox saying that I want to use a different format, and then select the menu item from the pop-up menu.
A much easier way would be to ditch the checkbox (it's redundant) and allow the user to select the default output format in Preferences. If the user wants to shift to a different format, then they just use the popup menu.
I have the impression from going through the old discussions on this topic that people felt that it was too easy to accidentally save the file in a collapsed-layer format. If you save your 30-layer Pixelmator document as a JPG, all those layers get squashed together, and you just lost a lot of work. Perhaps this is the motivation for the constant nagging about saving in Pixelmator format. I think that this accomplishes nothing. If the user is hell-bent on screwing things up, you can't protect him from himself. There's plenty of protection by setting the default output format as Pixelmator, but allowing a user to select a different output format in Preferences.
Please, stop trying to force me to save everything in Pixelmator format! Let me choose the format I want without having to jump through a bunch of hoops.