Dear Apple, I consider saving in your own format a document opened in a different format, a diversion of the customer's will, especially when it is not stated clearly. Hijacking documents to your own place with no warning.
I have been bit by this the first time, and the result was people calling on the phone to ask what happened to my updated version of a document. It was in the folder, with a different extension and format, as I found out.
In other words (pun not intended), I think that documents created in Pages should be saved as pages, documents created in a different format should be saved in the same format in which they were opened, as Joe Customer expects.
For now, I think that my workflow will be keeping documents shared with my colleagues in the shared folders in which they come, saving my working copy in Pages and iCloud, so that I can share everything with my iPad, and exporting on the original when I am finished. It is not optimal, but it should work, considering that there is not much concurrence in my workflow: I own the document until when I am finished.
Still, I am asking that a document opened in a different format should be saved in the same place and format, saved as in the format you choose, with Pages own format as default, and exported as usual.