A similar situation developed some time ago with hotels in Delhi. The tax authorities were reportedly not entirely happy trusting hotels not to fiddle their books, so insisted that any occupancy of a room should be taxed at a percentage of that room's "rack rate" rather than the zero rate for award stays.
The result was a hefty charge on "free" stay at some hotels, and quite barmy extra charges for upgrades. Whether the hotels taking advantage of an unenforced edict, and pocketing the tax, I don't know: yet each time I kicked up a fuss, I got a refund from the hotel.
I'd hate to cast British Airways in the role of a Delhi hotel, but from the OP's evidence the parrallel seems clear.
If the airline has been making a mistake, it will be grateful to learn of this through FT so that it begin to make restitution to any poor soul who has been overcharged
I'm sure they are keeping tabs on the tax-take for Brasil-originating travel, for the same reason.