Yes the Senior Preferred is equity. But equity owned by Treasury, not Fannie. Thus it's a debt, obligation, liability. There is a reason the deficit side of the balance sheet is called "Liabilities and Equity". It includes equities issued or sold by Fannie, and that someday need to be bought/paid back. Thus they are a liability.
It's pretty clear on the balance sheet: Fannie Mae stockholders’ equity (deficit): Senior preferred stock, 1,000,000 shares issued and outstanding 117,149
But it really does not matter anyway. It's only a difference of 117 billion dollars. It would only affect the stock price by about $100/share so I guess it's not important to understand it.
Again, the Senior Preferred Stock never shows up in the Liability section, because they are Equity.