POSSIBLE big spoilers
Probably a bad idea, but whatev.
I can clear up some of that for you if you're alright with it. As you seem to know already, all mediums of Black Rock Shooter are set in a different universe. The manga, the TV series, the OVA, the other two manga series, the game, etc. Unfortunately, that leaves huge gaps in continuity between them all, which kind of sucks in most cases because it makes things harder to keep track of. It wouldn't be best to consider anything canon, since the creator of BRS and the gang has never created a story for them ever.
For instance, Mato is a character centric to the TV and OVA universes, just like Yomi, Kagari, or any of the other "human" counterparts in the series. You'll find they don't exist anywhere else. Same goes for all BRS' you see in each medium, they are all different characters and not one of them are the same.
In the game, the male characters aren't very much important at all, they are sort of there to enforce the plot, to make the world seem more human and reasonable, since the game takes place on Earth after all. You will never find as many males characters as you do in the game in any other BRS universe. Unless you count the few you see in the OVA and TV series worlds. On another note, the male aliens are just what they appear to be. Bosses in the shape of males for some reason or another on part of the writer. I find it hard to believe they are a genderbent or alternate version of the other BRS girls, since there are many differences between them aside from similar color palettes and smaller unimportant instances that aren't really conclusive in determining their existence.
The flashbacks denote something important you'll find out later on about the BRS of the game world. What it is, I won't spoil for you. Hopefully, even through the language barrier you'll still be able to understand what they mean as you continue playing, because the game is one hell of a ride once you get further into it.
Though I said the worlds aren't necessarily interconnected, I still think you should give things like the manga and the OVA a try to really understand how different everything is in the BRSverse. In the end it'll depend on your opinion and views on the matter, but you may find that you get a much better experience from another BRS medium rather than simply the anime. In any case, I hope that made something even a modicum clearer than it was before. I know this is horribly long, but whenever I see something regarding BRS I get a little excited. I can answer just about any questions regarding anything BRS too, since I'm rather well versed in what happens with it. If you weren't bored or horrible confused by my post, feel free to ask anything else you'd like to know.
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