Now I got to think a few things while looking at it, it's .... fishy.
First of all it can be reffering to something else, like the Boss in the game, or what ...
Second, it can be what we think we think, a subtle hint, but then, the marketing team got it wrong because Samus is a She.
Now we can ... by looking at the circumstancial evidence conclude it may be a hint, because the next Metroid message is about a general topic, not necessairly a gameplay progression help question, so that "he's back" may not be necessairly in context of a gameplay event.
Then if we even take another step further you can see the Mii that's used to say this, he has his arms up in a "winner" position, are you thinking what I'm thinking.