Firstly: An OS can be a VM. Any turing complete machine can run an OS. Not a traditional one, but an OS nonetheless.
Same with the GPU thing. If it processes graphics, it's a Graphics Processing Unit. The first GPUs were text based in real life, though they weren't really called GPU and rather video controllers. The first "gaming" GPUs in consoles worked on a sprite based system, which don't draw lines and polygons either.
The formal, real life definitions don't quite apply in Minecraft as strictly. When someone claims to have built a car in minecraft, and they made some crazy complicated moving contraption with command blocks, do you point out that it lacks seatbelts, headlights, etc. and therefore does not classify as a road legal vehicle? No, because that doesn't apply in Minecraft. When someone says " I built an X in Minecraft", they're actually saying "I built a device that is similar to what we know as X in real life", or rather, a simplified version, appropriate to the simplified world of Minecraft. The same applies here.
Though then again, where do you draw the line? Many claim to have built a PC in minecraft that doesn't actually run programs. Does that count? Perhaps as a PC, but not a a computer. It's complicated.
Finally, it would sadly seem that this computer project's been abandoned for a while, so there's not much point in arguing about the naming of the components.