They are not basing it on a full J ticket IME, but on the cost of the same theoretical ticket should it be purchased. i.e on a UA flight from JFK-SFO it will not base the tax on an F or FUA fare basis, but on a HUAUP fare, should one be valid and available for purchase.

Regardless IIRC, the US transportation tax should not be charged on a through ticket when the end is not in the US (or within the Canadian 225 buffer zone). BD are having a laugh.