I'm about to speedrun this game and I was wondering if it's allowed to speedrun with another person speedrunning the same game, we were hoping to be in a call and speedrun together at the same time.

if you are refering to this as a race then sure, it's allowed, and you can submit if you both record your runs. if you are refering to completing a run where you complete only one part and another part is completed by someone else then it's generally not allowed in single player runs.

no i mean just two people running at the same time while talking in a call

Following on from NoobSalmon's post, yes you can both be in a call and run your individual copies of Black Flag at the same time.

aight thanks for the help