That's not true. I forgot where I saw it, but Goodman was the first company to pay the fee. They did indeed pay for it. Maybe because they're the only ones that's why they got special permission as a sort of thumbing their nose at those who didn't pay.
They couldn't possibly prepare all those products so quickly after the release of the public GSL unless they were bigger than WOTC, which they're not.
I also just remembered that Paizo paid and were disappointed by what they saw, which is why they created the Pathfinder line.
By the way $5,000 is a drop in the bucket for an investment to any company. It helps them decide yay or nay early instead of getting in on it late, as getting in early could earn them a heck of a lot more than $5,000.