You can't control how things are triangulated in maya without actually connecting those edges. In this case I would probably connect them as tri to form the point of the spike correctly, because at export to game you don't really get a choice to lock in the tri direction any other way, and you might get those edges being…
It is fine, it is not going to cause any problems. One thing you mentioned is that the smooth tool is creating the quads. That's not something the smooth tool does - it only averages position of vertex between its connected vertices. It doesn't create anything new. So if it appears that new edges were created that just…