I've never used a Microsoft system as a server myself, so I can not say anything about whether Windows servers are going to vanish, but just from the things that you're interested in with respect to the Pyra I don't think that you personally would really want to do network administration with Windows. The philosophies and ways-of-life behind working with Windows and working with FOSS tend to differ quite significantly (though of course there are reasons that both worlds exist, and in the same world no less).
I gotcha. Hopefully the 4 year institute will have more diversity.
You /
really/ should look into this, this is an important choice which you will be making soon.
My advice would be that you setup another VM with Linux. Ubuntu would be fine unless you prefer something else (but in the case of Ubuntu heed the advice at
https://fixubuntu.com/). You may also want to look into
Debian though, a Linux-based OS with a more "classical" spirit. Debian is what Ubuntu is based on and what will be preinstalled on the Pyra, too.
With VMs, one of the best aspects for learning of course is that you can create snapshots of the installed system that you can easily revert to so that you don't have to fear breaking anything, and you should make use of this. Try to just use one of these VMs for all your day-to-day tasks too, and then you automatically won't be limited to just installing and trying out programs in Linux.
Here are some free networking- and Linux-related learning resources which you might find helpful in determining just what exactly you find interesting (I don't have any relevant Windows-related resources at hand which I could give you, sorry):
...if you have more questions, then don't be afraid to ask them. If you want to increase the chances that you're going to receive helpful answers, consider
How To Ask Questions The Smart Way.