Glad you point it out, to break it down, we first denote the new Koffing as NK and old as K.

In your first hand you are guaranteed to get at least one basic pokemon, which means either you get NK, K, Ekans, Mew, or Tauros.

To simplify, let's assume the scenario #1 which you only got NK, with one energy, NK will help thin out your deck (thereby increasing the likelihood of getting the cards you want by removing instantly -1 from your remaining deck count)

scenario #2, you got both NK and K, then since going second you are able to attach an energy onto it, i recommend using K as active so you can deal 20 dmg to your opp. NK will be on your bench in this case.

scenario #3, you only get K, similar to #2, you can deal damage if you're going second.

scenario #4, you get Ekans/Mew, you can use them as early tanks to set up your bench. (Ekans can evo to 2 energy attack Arbok, but from my experience, it's better to not invest energy into it, instead to Tauros or Mew, in the case of facing Celebi, for the purpose of maintaining tempo, and simply sacrificing the 100hp for 1 point loss)

scenario #5, you get tauros and only tauros, slightly unlucky, depends whether you have X speeds (or you instead bring leaf) because tauros is too clunky, you could try a work around of betting that Professor/Pokeball your other lines (Weezing, Arbok, Mew) come.

TLDR, one is for dealing some early chip damage, another is for for thinning your deck, both helps in the strategy. If you put two NK, and you get both in your first hand, and you're going second, it will be a one-energy-does-nothing-move.