We don't know how strong the relationship between these companies is. One possibility is that Bitfinex wants to allow customers to immediately withdraw any USD deposits to other exchanges that accept Tether-USD. If that is the case, then effectively all deposits into Bitfinex are immediately "sold" to Tether in exchange for Tether-USD. That would mean that Bitfinex does not have any USD at all. Therefore the balance of USD in Tether's bank accounts would include all Bitfinex deposits.
Except for the opacity involved, nothing here would actually be misleading or obviously unethical; whether it is illegal is another question.
While I am not ruling out any shenanigans (and would only really trust an audit from a big 4 firm, if that), the report says that their cash is unencumbered. From investopedia [1], "Creditors do not have any claims to assets that are unencumbered, as there are no associated debts relating specifically to the assets."
> FSS makes no representation regarding the sufficiency of the information provided to FSS and all inquiries made by FSS have been directed to the Client and/or third party personnel responsible for maintaining such information, and the data has been obtained from the Client and/or third party personnel responsible for maintaining such information.
In other words, "unencumbered" here means "Tether told us they're unencumbered".