The only way that QL wouldn't be a part of the quake series is that it isn't new or different enough too be called quake 5. But with that way of thinking GTA: Vice City wouldn't be a part of the GTA series.
I think he is trying to say that QL isnt a brand new quake game but more of an overhaul to an existing one. Regardless though it is still part of the quake franchise just like niche star wars christmas specials are part of the star wars franchise and the animatrix is part of the matrix franchise.
Everything made under the quake banner by the people who own the rights to quake is part of the quake franchise