### 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
print_verbose(vformat("XInput %d.%d not available (server supports %d.%d). Touch input unavailable.",
				XINPUT_CLIENT_VERSION_MAJOR, XINPUT_CLIENT_VERSION_MINOR, xi_major_query, xi_minor_query));
	}
	xi.absolute_devices.clear();
	xi.touch_devices.clear();
	xi.pen_inverted_devices.clear();
	int dev_count;
	XIDeviceInfo *info = XIQueryDevice(x11_display, XIAllDevices, &dev_count);
	for (int i = 0; i < dev_count; i++) {
		XIDeviceInfo *dev = &info[i];
		if (!dev->enabled) {
			continue;
		}
		if (!(dev->use == XISlavePointer || dev->use == XIFloatingSlave)) {
			continue;
		}
		bool direct_touch = false;
		bool absolute_mode = false;
		int resolution_x = 0;
		int resolution_y = 0;
		double abs_x_min = 0;
		double abs_x_max = 0;
		double abs_y_min = 0;
		double abs_y_max = 0;
		double pressure_min = 0;
		double pressure_max = 0;
		double tilt_x_min = 0;
		double tilt_x_max = 0;
		double tilt_y_min = 0;
		double tilt_y_max = 0;