the other factor is DTC/CEDE. they are supposed to balance to the transfer agent- if they dont, which did happen 10+ years ago sometime, this casues all sort sof issues tehse days previously it did happen but DTC figured out the liability they were running and cleaned up tehre act a lot mroe than a decade ago.
a company can always look at both their OBO and NOBO records and figue out where the imbalance is- and force a resolution by several means. and DTC with their arcane process of putting chills and global locks has their own ability to resolve these situations.
i am not saying there arent shady operatros who try to scam the system
but if someone were naked shorting a stock it causes an immediate imbalance on DTC records which company if they are attentive can figure out quickly with NOBO AND OBO records. These are available by broker-and by looking at over the relevant time period compared to transfer agent totals for the balance at CEDE/DTC- and can then be used to track down where the short came from.
finally a company and force a resoluton also by changing the CUSIP numberand calling in the DTC/CDE certificate,or in some instances declaring a dividend can achieve same result. So companies whining that some mysterious and nefarious naked shorting is hurting their stock do have tools to combat this.so why dont they ? because their stock is not being naked shorted, but it amakes a good story
that buyin site uses a formula that they believe shows naked shorting but it is not based on amount of shares actuallybeing shorted but some formula they have devised. ( this is what was explained to me, perhaps they do have a precise way of measuring that i am not aware of).
--just think of it, if you were running a company with massive shorting going on, would you pile ,in-change name of company thus CUSIP number to force the shorts to cover ?