I submitted a 100% all souvenirs run but I realised the rules aren’t clear on when the time should end. In my run I got the last phantom medal after I 100% the last level. Should I have ended the timer when I finished the level or when I got the last phantom medal? Sorry if this is a stupid question.

It's a good question! I would end the timer after you finish the last level, as even then all the levels are gold and the game is already seen as 100% in the title screen. So what you did was good.