I suspect this was the case. Hypothetical example: Class A shares were available for $100 each, and Class B shares for $0.0001 each, but you could only get a B share by buying an A share. With the implicit (or explicit?) promise to merge the share classes together eventually to cause the prices to converge and massively inflate the Roth IRA side of the investment where you stashed the B shares.
So the $0.0001 shares all cost you $100 each to buy, but that $100 comes from outside your $2000 contribution limit.
But multiple share classes often exist anyway for various reasons (different preferences upon liquidation, different voting polices, different retraction policies, different dividend policies, etc)
I believe Bain Capital used separate share classes to pump their employees 401ks
That level of collaboration and financial engineering should be encouraged
The fun thing about your second paragraph is that courts don't care whether it is true.
Or are you claiming that on the day that he paid $0.001 per share, someone else paid more per share? If that didn't happen, there is NO WAY to determine after the fact what the “true” market value was on that date.