The Curse Client just downloads the .zip and unpacks it for the user.
If you mark something as "required depedency" in .pkgmeta, it will *not* be packaged. Its just meta-data for the Curse Client, so that it knows to get the package you specified as well.
I do wonder if it would be viable to remove the files of the "stub" addon from the fingerprinting done to identify addons .. however that would again be a Curse Client specific fix, that won't hold up if you ever decide to publish to WoWInterface, for instance.
We had automagic repacking with the old packager, and it was decided to not implement in the new one. There have been many issues where a library update broke addons and the author didnt even know because it was repacked silently. Now the author is aware which version is in his addon. Stuff may still break due to onthefly lib upgrading, however the standalone zip is guaranteed to be what the author designed it to be.
On your packaging issue: the biggest issue with it have the update clients. They use file signatures to recognize the addons you installed. If such a "library" is part of multiple addons, it would need some extra special logic or metadata to handle that. If you install a second addon using that, which happens to be sbhipped with an older version of it, do you blindly overwrite?
There is a ton of problems with this, thats why most auhtors try to stay away from that design. The best solution for updaters is the use of real dependencys, so that the client can manage the library as a seperate addon. However, that will require people that download it from the website to manually download the library, as its nop longer packaged. However they would always have a recent version and not something that came with the zip.
Another design would be to force addon authors using your lib to provide the SV for it. But that opens another can of worms.
Implementing in the future. Well. The packager is opensource and if we can come up with a proper way to handle it, there is no reason not to implement it and send a patch to kaelten. However, that would need additional client support, which is really the hard part. And you still screw over website-downloaders, as they would still blindly overwrite no matter what version it is.
As a final thought, it doesnt matter if you package manually, or let the packager do it. The problems remain the same ;)