IANAL, but I believe you are misinterpreting the clause - the clause disqualifies an officer or 10% shareholder of (subparagraph G:) a corporation that is >= 50% owned by (subparagraph A:) a fiduciary (owner of the IRA).
No only owning shares in their IRA of the company they're directly an officer in. It's limited in scope to essentially people with significant control in a corporation.
But Thiel did not own >= 50% of PayPal.