After you respawn, what's the first thing you want to do? Regroup. In a competitive gaming environment every second counts. Using the motion tracker to see where your squad mates are will help you regroup faster, no doubt about it. This also increases situational awareness by having more information about where the other marines are. Would the motion tracker work "better" if it never detected friendly movement? I don't know. I'm not the one who has been testing the mechanics. Gearbox does that in house.
To create an authentic experience, I imagine that trade offs and compromises are to be expected. Visual aesthetics do not dictate an authentic experience alone, as it works in tandem with gameplay mechanics. I don't care if the game is treated as a canonical addition to the "aliens bible" or not. In the end, that doesn't affect the actual experience of playing the game. I can say the game is not canon simply because the motion tracker has red dots, but if the gameplay mechanics themselves work to deliver an authentic experience while I am playing then I don't care. So these changes they made, if it works towards improving the gameplay as an authentic experience, it can be a good thing.