For those of you who wish to use the old YouTube Android TV app because the new one sucks (for example, you can't sign in to a brand account... ie, a sub-account), I have figured out how to disable it auto-updating without disabling auto-updates in the Play Store.

Step one: go to your system apps and uninstall updates for YouTube. Then disable the app.
Step two: download the YouTube for Android TV 1.3.11 apk and install it.

I used to have to uninstall the YouTube update every day. I followed these steps last week and so far it hasn't updated. I figured that installing the apk outside the Play Store would do the trick, but I wasn't sure what would happen with disabling the system app YouTube (because it comes with my NVIDIA Shield and I believe it also comes with the Mi Box). Everything seems to be working great.

Edit : I'm such a tool. Apparently my son has been uninstalling updates every morning before I was even awake. So I thought the entire time that my fix had worked. Sorry about getting all your hopes up!

Another edit : skynet_watches_me_p says:

if you have the developer tools turned on, you can install and lock packages via ADB interface. Install the 1.3.11 APK and lock it using adb.

I am going to attempt and then post my results!