Comment 4 for bug 1656509

Then that's very strange. I fixed this exact symptom for Adwaita already in:
https://bugs.launchpad.net/terminator/+bug/1599453
If you search down through the comments you will see me mention the grey box around the title bar under Adwaita. I spent quite a bit of time finding and fixing various transparent rendering issues, culminating in the merge of a decent chunk of work:
http://bazaar.launchpad.net/~gnome-terminator/terminator/gtk3/revision/1672
Specifically for this issue the fix was in terminatorlib/terminator.py, lines 417-424.
That change fixed the rectangle for myself and the OP on 3.18. It makes no sense that it doesn't work for you, as it is a cross theme fix, and you are on a newer gtk. The best I can suggest is that you use:
GTK_DEBUG=interactive terminator -u
and see if you can find exactly what element in the hierarchy is introducing the grey box for you. Otherwise it's a case of randomly making changes in a probably futile attempt to fix it.