I just did a fresh install of VS2015CE and MonoGame 3.5.1 and had the RT issue, used my above method this time allowing VS to open the .vstemplate file and just did as before and removed the reference.
EDIT
OK! Found the actual issue, the WinRT token is included twice… did not notice this in word-wrap on notepad but I saw it in VS. so just remove one of the references.
/EDIT
Works like a charm.