Created attachment 138343 [details]
Partial screen image illustrating the problem
macOS High Sierra version 10.13.3 (17D102)
XQuartz 2.7.11 (xorg-server 1.18.4)
xset +fp /usr/local/fonts/misc
xrdb -merge ~/.Xresources
All native macOS windows have a top limit that leaves a visible gap between the window and the menu bar. X windows have a top limit that leaves no such visible gap.
See attached image illustrating the issue.
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