Ford wanted out of the tranny building business, so they sold all the tooling and rights to produce the Top loader (and the other Ford tranny the "303") to Tremec in 1973. Regardless of who made it, it's still a Top loader.
Tremec was an OEM supplier to Ford and Jeep through the 80s. Tremec designed the TR-3550 on their own nickel, with no OEM contract. It was intended primarily for off-road trucks. However, they had to make it versatile enough to sell to any market out there which is why it has 3 potential shifter locations.
Dimensionally it is based on the Top loader, with the same gear spacing and mounting pattern, but you can't switch gears between the two, it has a 5th gear, and as mentioned the internal shifter was a unique Tremec design. Since at the time it was the only transmission Tremec made, there was no need to call it anything other than a "Tremec".
So I would say a Top Loader is always a Top loader regardless of who made it, and even though Tremec bought the entire transmission division from Borg Warner, everyone will always recognize the "Tremec" as the 3550 because it is the first transmission that was designed by Tremec.