My house is crimped PEX as well but have the piercing valve on the copper supply line between the meter and the PEX manifold.
The better way to do it though would be to either Tee into a PEX line, valve then ro unit, or if you have a spare line on your manifold tie into than. Just need to rent a PEX crimper (just did some PEX runs and minumin was about 10 bucks from HD).
The auto shut off at least the one I'm using shuts off the ro feed, if the ro output is closed.
Link to diagram of Aquasafe unit (it's the 4 port shuttle valve shown between the prefilters and ro). Have also read of people just hooking up a garden hose timer between the supply line and unit.