Are these one and the same company? If so why two names, different bottoms, or different models?

Same owner, same boats.
Regal had the Velocity name for a while.
I'm sure there are lots of people here that can tell you more details.

mine says both it is a thoroughbred by velocity

I believe they stopped calling them Thoroughbreds after 1996. Now just Velocity.... Same Company!

Velocity name was tied up in a legal deal between Steve Stepp and Regal boats, so Steve used the Thoroughbred tag for some years till it was resolved. The dual naming was used for a little while, '96 models were the last to have the decal showing both names as docbones said, '97's were tagged as Velocity's as the legal issues were resolved and Steve regained control of the name.

I actually thought the Thoroughbred deal was unique, each model was named after a race horse. The 26 was "Summer Squal", the 35 was "Majestic Prince", and the 41 was "Bold Ruler".