you are not missing anything. With a healthy supply of shares available to be sold, a MM will sell short to a buyer @ $.0001 and then cover the short by buying shares from a seller. Most likely the MM is buying at $.00005, making a profit/spread. The daily reports show the shorting that is going on, but does not reflect the fact that the short is being covered.
The twice monthly report accumulates the two week short data and matches it to what was covered, leaving the real short position.
The daily short report just reflects MM's confidence that they can easily cover the short from the supply.
On more liquid stocks, in fact, most likely FFGO in its heyday, MM's probably even carried a inventory of FFGO stock to cover the trade. But no MM wants to carry an inventory of a $.0001 stock that has nominal trading (e.g. real dollar value vs #of shares traded).