Just launch the juce demo, and toggle the “use native window title bar” option. The window gets resized , and is now slightly higher and wider (easy to spot with the checkerboard background)
Commenting the windowBorder stuff in LinuxComponentPeer::setBounds seems to fix that:
XMoveResizeWindow (display, windowH,
wx,// - windowBorder.getLeft(),
wy,// - windowBorder.getTop(),
ww,// + windowBorder.getLeftAndRight(),
wh);// + windowBorder.getTopAndBottom());