Even X had a separate application called xterm 42 years ago: the complete X system was not to my knowledge called a terminal system, except perhaps when discussing the dedicated client devices, such as VT1300. Also the term "virtual terminal" as far as I know has always referred to a the kind of interface this application is making use of.
So I think we can just accept that the term is overloaded such that "terminal" refers to both of these situations, as there is no historical precedent to have it exclude the other situation, and the term "terminal-based application" is completely clear to a rational listener.