The article doesn't address how Tengen is now able to produce unauthorized NES-compatible cartridges. Is Tengen paying Nintendo for a license? Did the patents expire? Did relevant legal precedents change? Another possibility might be that, while Atari's 80s legal actions established that intermediate infringement during reverse engineering could be fair use, Atari itself was precluded from relying on that fair use because its lawyers did naughty things. Maybe "new" Tengen reversed engineered it again from scratch without naughty lawyers?
Does anyone know?