And I'll just toss the theory into the room that the Shit Ninja (Shinja?) is MC's missing cousin. Because we know absolutely nothing about her. Likewise, we know nothing about Scarlett's sister April after 1999. But aside from the fact that it's quite unlikely that she's the Shinja, I'd like to note that she's cooperating with Masked Man and she helped us save the then-unborn Jessica, so I'm at least willing to give Masked Man the benefit of a doubt and assume that he's at least a neutral party in the plot, unlike the principal and the people who want to spy on MC.
The game has quite a few instances where adding two and two equals five.
Because there is often a crucial part missing/not told yet.
For instance you are saying the masked man is kind of neutral if not even helping the MC because he told him he would be able to save someone close to him.
But keep in mind he only told that to MC after he refused to go back.
He after the fact explained that big events can't be altered anyways so the sister MC saved wasn't in any danger to begin with according to that theory the masked man gave.
Unless it is some time paradoxon shit where MC has to be sent back to save his sister so that he could have a sister. Or even be born himself, as Jerk McJerkface was about to hit his Mom and that besides possibly ending the life of the baby would also be likely to start a depression in Tiffany.
I previously stated that maybe Luna broke off contact and ordered Skylar to do the same because "Donnie" was caught cheating.
It is possible that such a woman he caught cheating with is ousted from her family and that is the reason why April is not mentioned in 2019 anywhere.
Even a sort of witness protection BS wouldn't be totally out of the question.
Getting even more ... weird it could even be possible that April was a spy sent back to 1999 from 2040 or something and is actually the daughter of Alyssa and not Scarlets sister and that is why Alyssa did not remember having an aunt ...