That sort of misalignment is not uncommon with Pokémon cards from the Wizards of the Coast era (or from more recent sets, for that matter). Everything looks fine... the printing resolution of the card is crisp, the Energy symbols are not distorted or saturated, and, as you pointed out, the fonts and spelling are correct. It's the genuine article!
Not only is it real, but it's in near mint condition, so it will look the best it can in a binder (minus the centering). Some people would pay $20 for the privilege of owning a Near Mint, Unlimited Edition Dark Blastoise. Treasure it (Or I guess sell it if that's what you were planning on doing).