I'm doing all of my work with expansion PEX. I'm a little puzzled about how to finish the valves where the toilets and sinks connect. Are you supposed to just leave the plastic visible where the valve is sticking out of the wall?
Plumbing with PEX – How to Finish a Valve When Using PEX Pipes
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Related Solutions
Replacing the current pipe nipple with one that is slightly shorter is the best way to go here. The thing to do is to simply cut off the length of the current nipple by the requisite amount and then get that end threaded slightly more. The re-threading step is necessary because the pipe nipple threads are a tapered thread.
If you do not have the tools to re-thread the pipe yourself it is a service often offered by the bigger old school type hardware stores. A machine shop or plumbing shop are places where you could likely also get this service.
Edit:
It occurs to me that if you have only 9/16" of the pipe nipple projecting from the wall that it may be somewhat difficult for you to remove the thing using conventional plumbing tools. A typical pipe wrench would gnash the threads as you tried to remove the nipple.
There is a special tool just for this purpose called an internal pipe wrench that can be used from inside the nipple to remove the long one and re-install the shortened one. These are available from most tool suppliers including via Amazon.
Since you mentioned freezing in some comments, I recommend this:
This is a freeze-proof hose bib, complete with anti-siphon valve to prevent water running backwards from your yard into your supply plumbing should the pressure go off.
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Best Answer
Yes, the piping (which in your case is pex) will be visible from the wall or floor to your cut off valve. You can put escussion rings on pipe that lay flush against the wall to give it a more finished look.