I made a new engine a little while ago, and decided to only include the Stereoscopic 3D part to save money. After it was completed, I discovered that I couldn’t choose it for the game. Turns out that I needed another 3D part for it to be of any use. It would be nice if something was added to make it obvious (at least more obvious) that the part is an upgrade to normal 3D, and not a replacement.
One way to tell is that there is no version next to Stereoscopic 3D, but I agree that it would be good to know what’s a Graphics Engine and what’s an addon.
I always choose the top level of the old engine with the bottom of a new one if I switch (like from 2D to 3D, I selected 2D v4 and 3D v1 for my first 3D engine, just in case I needed to make some 2D hits) so I knew it was an addon through that.