I think it would rely more on building materials. The reactor cooking off supplies the energy to convert just about everything to a plasma, but color in flames and explosions comes from the presence of metals, not non metals. We already know the Terrans and Vasudans build differently (Serapis armor compared to Myrmidon or even Apollo Armor), why shouldn't there be a difference in the color of the explosion? I can see not changing HOW they blow up, but to say that every time a big ship, built by two different species blows up, that it is going to produce the same color of shockwave every time is somewhat, improbable to me.