Originally Posted by Sammy2
... The thing is I think that he's using the myPlex web app on Chrome. ...
if this is true, this explains why the PMS is transcoding. As far as I know, nothing plays natively through the Plex/Web. If you look the in PMS setting for Plex/Web, you only get to choose what bit rate to use. There is no option for direct play. It's just a limit of the interface. I don't know any services that play files direct via a web browswer without some kind of special plug in. I think they're just using HTML5, maybe Flash Player.
In the short term, assuming your son's machine has Windows7 or Windows8 with Media Center, just install Plex home theater and it will play the MKV directly.
Unfortunately, the way Plex is setup, if there is transcoding, it's done on the PMS machine. Doesn't matter what the front the end is on. The PMS is putting it in a format that is friendly to the front end machine.
As for the share email thing, that's just more to verify the machine is authorized to access your PMS. It also for setting up the IPs , and possibly, ports to access the PMS. That's why it's so easy to setup Plex and various front ends. Not like the early days of Plex for Android. It's leaps and bounds easier.