First of all, I must admit I have trouble understanding your writings. As a
consequence, I may have misunderstood you.
I am not sure you understand that, nowadays, most of the free applications
commonly used in a GNU/Linux distribution were not written within the GNU
project (and the proportion of code written by the Linux project, the kernel
only, is even smaller). For instance, the projects Linux-Libre and IceCat,
which are GNU sub-projects, are only about patching Linux and IceCat to
respectively remove proprietary blobs in Linux and invitations to proprietary
software in Firefox. Almost all their codes come from the Linux project and
the Mozilla project.
ABrowser is another Web browser, developed within the Trisquel project, which
essentially is Firefox minus the invitations to proprietary software (much
like IceCat).
KDE is not a GNU sub-project (GNOME is)... but KDE is free software and is
mainly released under the GNU GPL and the GNU LGPL (for the core libraries).
The fact that they adopted the licenses written within the GNU project does
not make it a GNU sub-project. The fact it is not a GNU sub-project does not
make it proprietary.
For instance, no "graphical system" has ever been written within the GNU
project because some versions of the X Window System (originally developed
within the MIT) have always been released under a free permissive license
(not written by within GNU project) and their was no reason to write a
replacement for this perfectly fine software (today, however, it shows
technical limits and the Wayland project, which again has nothing to do with
GNU, is about to advantageously replace it).
Trisquel's repositories only contain free software (if a proprietary software
sneaks in, it is considered a critical bug). This is a great advantage of
Trisquel: you need not fear installing proprietary software by mistake when
you take it from Trisquel's repositories.