Nick actually said that Headmaster has been seen briefly. "The War For Season 2" http://www.comicbookresources....
"Or is this a red herring? One thing we've established about the Headmaster – who's barely been seen at all – is that he's very good at deception. Irina has been wrong before."
'barely been seen at all'
I think that this means Albert.  Albert is right there at MGA under your nose.  Albert is the first to meet the new students. Albert could be the gardener and this would explain why one goes to The Greenhouse to meet Headmaster.Â
I gotta remember Alfred is Batman; Albert is Morning Glories.