More problems deiscovered from the problem child. :) I think these fixes should improve reliability across the board for reading focused windows though. Needs testing.

internal/platform/xorg/commands_native.c

@@ -188,8 +188,11 @@ static void cthulhu_read_frame_bounds(Display *display, Window window, Foregroun
 
     XWindowAttributes attributes;
     if (!XGetWindowAttributes(display, parent, &attributes) ||
-        attributes.class != InputOutput || attributes.override_redirect ||
+        attributes.class != InputOutput ||
         attributes.map_state != IsViewable) return;
+    // i3's decoration windows are override-redirect: that flag bypasses WM
+    // management, not foreground ownership. Validate the enclosing frame by
+    // its tree, managed children and bounds below instead.
     Atom stateAtom = XInternAtom(display, "WM_STATE", False);
     Atom type = None; int format = 0; unsigned long items = 0;
     unsigned char *data = cthulhu_window_property(display, parent, stateAtom, &type, &format, &items);

internal/platform/xorg/frame_foreground_native_test.go

@@ -62,6 +62,8 @@ func TestNativeReparentedFrameForeground(t *testing.T) {
 		{"resize", "client", [4]int{0, 0, 1000, 700}},
 		{"move", "client", [4]int{-30, 40, 1916, 994}},
 		{"border", "client", [4]int{0, 0, 1920, 998}},
+		{"i3-frame", "client", [4]int{0, 0, 1916, 994}},
+		{"i3-run-dialog", "client", [4]int{0, 24, 1916, 989}},
 		{"other", "other", [4]int{2000, 0, 500, 400}},
 		{"plain", "plain", [4]int{}},
 		{"shared", "shared", [4]int{}},