The Transfer agent holds the list of all investors and share count on a direct feed from all brokerag houses (this is for various reasons 1) stock record 2) dividend payments if applicable 3) restrictions on stock i.e. 144, legends,etc 4) central depository for control of inventory. A brokerage firm can open a confidential account so that all reporting is under the SSN, but nothing else discloses the investors name EXCEPT the brokerage house has limited internal platforms/screens that would show the persons name (i.e. Their person financial advisor and sales assistants can view). My understanding over the years is the Transfer Agent DOES NOT see these types of investors details, just quantity.

Confidential accounts are VERY common and have seen it at internal employees of the brokerage firm using it to celebrities or politicians.

Transfer agent would only release the stock record to authorized individuals set up at BLTA and/or and regulatory body requesting (SEC, FINRA, OCC etc)