I'm wondering why this has not been fixed after such a long time. It can at 
least be improved easily.
If the Adwaita theme works (which it does in may case, too), then it is (at 
least partly) a theme issue.
In fact, some defaults seem to be missing in the Ambiance and Radiance themes:

By setting a default for the text background color in the following
file, most problems (gnome-calculator, gedit) are resolved for me:

/usr/share/themes/Ambiance/gtk-3.20/gtk.css:

textview text {
   background-color: white; }

@import url("gtk-main.css");

However:
* Some problems remain., e.g. emacs scrollbar background color broken, too.
  The following solves that partly, too, but not completely:
  scrollbar {
   background-color: white; }
* If you change such system files, they will get reset with some later system 
updates.
  (dpkg-divert can help to prevent such resetting/updating of files)

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https://bugs.launchpad.net/bugs/1760818

Title:
  gedit and gnome-calculator transparency/graphics corruption issue when
  GTK_IM_MODULE=xim is set

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