See this post
https://forums.macrumors.com/showthread.php?p=18850781#post18850781 for details on what I am talking about.
Does anyone here have the 5.1 update to Pages, and does anyone know if the original bug in the above link has been fixed?
I have 5.1, and this is not a bug, it's a feature. Bugs are technical flaws - something that doesn't work as it was designed. The behavior of Save and Export are very much intentional.
We don't find 100% consistency between Apple apps, but the trend is:
Save - save in the app's native format, with the current filename (preserve the work you've been doing)
Export (OS X apps) - create a duplicate the document in a different format (the alternate version will be retained in the file system/network)
Send a Copy (iOS and iCloud apps) - email/message, etc. a copy of the file, optionally converted to another format (the copy will not be stored on the device or in iCloud).
Duplicate - make an exact copy of the file (mostly intended for creating divergent versions).
I think part of the issue with Pages and Numbers is that they're tied into iCloud. It makes a certain sense to Save only in the native format, as those documents may be edited in OS X, iCloud.com, and iOS. Copies in alternate formats do not accumulate in cloud storage, and there are potentially fewer versioning problems. If you drop a Word doc onto iCloud.com, the file browser initially shows it as a "W" - once the file browser shows a thumbnail of the document, it's been converted to Pages format, and the "W" is nowhere to be found.
Overall? If, like most of us, you've learned that Save As is the way you convert formats and create divergent versions of a document, this can be a bit of a pain - more options in the File menu, different keyboard shortcuts, etc. Personally, I'm good with it - there's a bit better clarity of purpose, which happens to help me a little, but probably helps newcomers far more.