### 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
_update_size_hints(p_window);
	
	XResizeWindow(x11_display, wd.x11_window, size.x, size.y);
	for (int timeout = 0; timeout < 50; ++timeout) {
		XSync(x11_display, False);
		XGetWindowAttributes(x11_display, wd.x11_window, &xwa);
		if (old_w != xwa.width || old_h != xwa.height) {
			break;
		}
		usleep(10000);
	}
	
#if defined(VULKAN_ENABLED)
	if (context_vulkan) {
		context_vulkan->window_resize(p_window, xwa.width, xwa.height);
	}
#endif
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->window_resize(p_window, xwa.width, xwa.height);
	}
#endif
}
Size2i DisplayServerX11::window_get_size(WindowID p_window) const {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), Size2i());
	const WindowData &wd = windows[p_window];
	return wd.size;
}
Size2i DisplayServerX11::window_get_size_with_decorations(WindowID p_window) const {