Congress included the penalty to get the private sector insurance companies on board with ACA. In other words, Obama knew no insurers would join in if they didn’t have some guaranteed revenue to take on pre-existing conditions, no cancellations, and no lifetime caps.
Congress further added the Severability clause to give the insurance companies a way out if the Rube Goldberg, penalty is really an income tax thing, fell. The insurance companies would then lose that revenue but still be stuck with essentially unlimited risk.