### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
XWindowAttributes xwa;
			XSync(x11_display, False);
			XGetWindowAttributes(x11_display, wd.x11_window, &xwa);
			ERR_FAIL_COND_MSG(p_window == MAIN_WINDOW_ID, "Main window can't be popup.");
			ERR_FAIL_COND_MSG((xwa.map_state == IsViewable) && (wd.is_popup != p_enabled), "Popup flag can't changed while window is opened.");
			wd.is_popup = p_enabled;
		} break;
		default: {
		}
	}
}
bool DisplayServerX11::window_get_flag(WindowFlags p_flag, WindowID p_window) const {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), false);
	const WindowData &wd = windows[p_window];
	switch (p_flag) {
		case WINDOW_FLAG_RESIZE_DISABLED: {
			return wd.resize_disabled;
		} break;
		case WINDOW_FLAG_BORDERLESS: {
			bool borderless = wd.borderless;
			Atom prop = XInternAtom(x11_display, "_MOTIF_WM_HINTS", True);
			if (prop != None) {
				Atom type;
				int format;
				unsigned long len;
				unsigned long remaining;
				unsigned char *data = nullptr;
				if (XGetWindowProperty(x11_display, wd.x11_window, prop, 0, sizeof(Hints), False, AnyPropertyType, &type, &format, &len, &remaining, &data) == Success) {
					if (data && (format == 32) && (len >= 5)) {