That's incorrect. Wall Street thinks the Alibaba stake, Yahoo Japan stake and its cash holdings are worth less than their face value - as is always the case (see: how EMC's VMWare stake has always been discounted historically). For numerous reasons, the most obvious of which is: investors can never realize the entire face value of those holdings, so they never give a $1 to $1 value to them.

We can simplify this really fast: give me one example of a public company of even remotely similar financials trading with a negative market cap in the last ~30 years in the US equity markets.

Tons always have. Look up the valuation of Macy's real estate; it is about 2x the market cap. Even adjusting for the full EV value its at a discount. They would realize more value by shutting down the retail business and selling off the real estate. But investors feel the chances of that happening are slim to none which leads to the low valuation. Yahoo is a tech company but revenue, growth rates, net income and free cash flow are common to all companies.