X.Org vs. XQuartz - MacPorts

In general you are confusing several things.

XQuartz is a set of libraries to allow X11 applications to be compiled and run on OSX. It is based on the X11 sources from X.org the changes were originally done by Apple.

Quartz is the set of technologies that are in the OSX Core Graphics that deal with 2d from wikipedia

Quartz is often synonymous with Core Graphics

Thus Quartz is so called as it provides the X11 libraries that work by calling Quartz provided APIs

In the macports variants.conf what you are saying is don't use X11 (i.e. XQuartz) but use Apple's graphics directly and not via X11 so not calling any X.org code

If you want to keep independant your future upgrades of XQuartz and MacPorts, then you will have to keep both installations.

XQuartz is installing libraries, binaries in /opt/X11.

MacPorts is installing sources, configurations, dependancies, libraries, binaries in /usr/local or where you prefarably decided to configure it. In my case to avoid any risk of confusion with other package managers, I configured MacPorts to work on the base of the rootdir /opt/local.

If you remove a needed library within the install path of MacPorts it will have to rebuild it. On the other hand, it will never upgrade anything when you modified the XQuartz version because it is outside of its managed source and install tree.

This practical way of managment stand without problem since Snow Leopard up to Sierra.