Hello, gemforce.
As we state in the “Connections” section of the product page for the sensor, the XSHUT pin is not 5V tolerant, but there is a resistor on the board that will pull the pin to 2.8V, so you can toggle the state on a microcontroller like the ATmega328p that is running at a higher voltage by toggling the gpio pin between a high impedance state and actively driving the GPIO pin low.
We do not have any specific recommendations for using the sensor with a cover, but ST has an application note for using one that includes a specific manufacturer’s part.
-Nathan