Starting from the bottom of page 14 (emphasis added):
If the junior shares were redeemed in full before the senior shares (for reasons explained in the previous section), the GSEs would be able to pay only $48 billion for the senior preferred shares, CBO estimates, far below their face value. In that scenario, the Treasury could exercise its warrants for common stock, but it would receive very little value for them, CBO projects. The reason is that the shares that the Treasury would purchase through its warrants would represent ownership of only a small portion of the GSEs after the sale of stock to new investors—an effect known as dilution
And on page 16 (emphasis added):
That equity valuation would be large enough to cover the expected capital shortfall of $172 billion and the $35 billion in outstand-ing junior preferred shares, leaving about $98 billion to pay the Treasury for its outstanding senior preferred stock.34 In that scenario, the Treasury could exercise its warrants for common stock, but it would receive very little value for them, CBO estimates, because of the projected dilution of existing shares.
Short version: the $48B and $98B value estimates are for the seniors, not the warrants, and scenarios leading to those valuations leave the warrants, and thus the existing common, with "very little value" using CBO's own words.