Parliament can't directly negotiate treaties with foreign powers. It's just not possible, that's a function of the executive. Parliament can approve or disapprove of such treaties but can't determine what the executive wants to do. The same goes for the referendum and is why it was a stupid idea. No referendum can require parliament or the government to want to do something, or specify exactly and unambiguously how they should go about doing something they don't want to do.

With the benefit of hindsight, it all worked out well for Johnson: he cowed the party, could renegotiate without much fear of the ultras, and could choose the circumstance of the next election to his best advantage.

The methods he chose to achieve this, though, greatly weakened parliamentary sovereignty.