The "Emerald & Radiant Cuts" chart from Accredited Gem Appraisers shows class 2A and 2B (international fine trade cut) to have depth and tables between 59 & 69. However, on http://www.goodoldgold.com ,the emerald cuts he features which are "super-ideal fancies" have 71.3/64, 75/69 and 70/69 depth and tables, which would put them in the 3A or even 3B class.

Each of the three stones on the site look beautiful and perform outstandingly on the Brilliance Scope, but don't score so high on the cut class guide I've been directed to. What gives? Can I get a 3A cut or 3B and have the kind of brilliance that I want? (I know, an emerald is the least brilliant cut, but I would like to maximize the brilliance that is available in my clean-line beauty.)

It looks like you already got an answer form David Atlas

AGA charts give you the best starting point available today but as David pointed out the work on cut grading is far from completion especially for fancy shapes.

Keep in mind that Brilliance Scope is not an ultimate tool either

I think if you have seen and like the diamonds, it's all that counts.