Couldn't one say the same thing about the Ice type being a second Water type in that manner?
I'll defend the position that each type is and always was intended to represent something unique and distinct. Otherwise, why even bother including them?
If they were combined a lot at initially, that doesn't mean that it's because they're practically indistinguishable, as Grass/Poison and Water/Ice are at least as numerous from the beginning. The fact that there were "exceptions" that were pure types of a type from these combinations also doesn't fit that (Ground has Sandslash and Marowak, jsut as Grass had Tangela, while neither Rock or Ice had any pure types originally), neither do the same types being used for making different combinations (Rock&Water, Grass&Psychic etc...).
So they were thinking straight IMO. (and let's not bring fossils into this, as they're a whole separate philosophical issue worth discussing and we're already far off-the topic..)
A good example might be comparing the two generic 3-stage Rock types that are basically counterparts: the Geodude-line and the Roggenrola-line.
The first has an extra Ground type, while the other one is pure Rock.
One of the differences between them is that Geodude is much more muddy/dirty, while Roggenrola is a clean dry mineral-based-creature with sharp edges.
The first thing I think about when I consider Zygarde's typing is the Earth-attributed Golden Center Dragon from Chinese astrology, who is the perfectly neutral being. The Center Dragon is the fifth element. It represents the changes of seasons and the neutrality of earth as the other elements confront and balance each other. If you consider that to be a possible origin, it kind of makes sense.
If not, you could say that Zygod, aka Zygarde's Perfect forme, who we assume is based on Hel, is like the germanic counterpart to Hades. I read a manga novel once that told a story about a handful of the Greek Gods and how they are the powers that be, and yet are affected emotionally and spiritually by a series of metaphysical cold-equations, the true "powers that be". In a conversation between Apollo and Hades, it's discussed how the world was divided up into three equal parts between the three brothers, Zeus, Poseidon and Hades. While it's normally a belief that Hades is merely the ruler of the underworld, Hades in this universe is omniscient about all living things on the planet, and their times of death. While Zeus rules the sky and Poseidon rules the sea, Hades is the true ruler of Earth for his connection to all of its inhabitants, a kind of parallel to Zygarde's ability to monitor the ecosystem. His appearance also consistently goes through slight changes (the horns/antlers on his head constantly shift size, shape and position), which is taken to be an artistic representation about the constant changes the lithosphere goes through between tectonic plates shifting, plants overgrowing each other, sediment compacting into new layers as new eras begin and end, etc.
Zygarde, as a Ground type, represents a common genetic trait shared throughout the world; the cellular structure of a carbon-based life form. As for it being a Dragon type on top of that...to me, Dragon is the element of lore and mysticism. The distinguished Dragons in the Pokemon world possess a kind of mystical power that defies more natural, tangible elements and their typical type matchups (having a fairly square number of weaknesses, resistances, and SE matchups).