that article is just wrong- see definition of "net equity" from the SIPC statute. It is the value of the cash and shares in the account as of the filing date (ie the date the broker holding your shares is liquidated) less any amounts you owe to the broker (for margin or other fees). As a practical matter, if you are missing shares or cash from your account, SIPC will go buy some shares and replace them and credit you with any missing cash, subject to the limits.
(11) Net Equity
The term "net equity" means the dollar amount of the account or accounts of a customer, to be determined by-
(A) calculating the sum which would have been owed by the debtor to such customer if the debtor had liquidated, by sale or purchase on the filing date-
(i) all securities positions of such customer (other than customer name securities reclaimed by such customer; and
(ii) all positions in futures contracts and options on futures contracts held in a portfolio margining account carried as a securities account pursuant to a portfolio margining program approved by the Commission, including all property collateralizing such positions, to the extent that such property is not otherwise included herein; minus
(B) any indebtedness of such customer to the debtor on the filing date; plus
(C) any payment by such customer of such indebtedness to the debtor which is made with the approval of the trustee and within such period as the trustee may determine (but in no event more than sixty days after the publication of notice under section 78fff-2(a) of this title).