First of all, I'm a newcomer to APL and even though I've hit 40 I feel somewhat like the new kid on the block. :-)
I haven't advocated plenty of new quad-commands or changes to the core language (although there are certainly a few of those that I'd like to see too, but I respect Jürgens wishes and vision for the project).
The native function interface was designed in order to be able to implement libraries that go beyond what the core APL language allows (file management is an obvious one, the SQL support being another, and the Emacs mode also needed to be able to communicate directly with the core interpreter through a back-channel which required yet another native library).
The benefit of the native libraries is that they are standalone and can be developed my anyone and they don't need to be delivered as part of the GNU APL distribution. My SQL library is a good example of this as it's completely separate (that said, if Jürgen is willing, I'm happy to see it included in the core).
All of the libraries that I suggested integration with would be implemented in a similar manner. It is no more an extension to GNU APL than libxml is an extension to C. It's just a library that happens to be implemented on top of a platform.
Like it or not, in order to be able to effectively use the tool (and even, dare I say it, attract some new user?) there needs to be an easy way to interact with the rest of the world. The world uses things like JSON, XML, spreadsheets and graphical monitors (notice the correlation with my list in the previous mail? :-) ).