It's not uncommon for one of them to not be at the condo for the night, sometimes they'll go to their own respective homes to see family (though they usually need permission from Eggman first BOOO)!!
Shadow lived with Gerald and Maria prior to joining the band!! Gerald has VERY high expectations for him, hoping that he could carry on his legacy and research after he retires (SHADOW DOES NOT WANT THAT!!! ) and as a result is fairly strict with him over a lot of shit and one of the main things is how Shadow chooses to present himself!!
Shadow loves alt fashion however Gerald DOES NOT, he'd made the mistake of dressing how he'd like once at home and never again!!! Now he makes an effort to dress rather formally around Gerald to make sure he doesn't piss him off.
So yeah the first time Sonic and Silver saw him in his more formal getup they're SHOCKED. They're so used to seeing him decked out in piercings and cool outfits that it's slightly jarring.
ALSO MARIA IS VERY MUCH ALIVE IN THIS AU - still ill but definitely not dead!!! If it weren't for her Shadow would not be visiting home regularly.
*Puts on my rareship classes* Amy, Shadow... I raise you another hypothesis : Princess Blaze. After all they didn't fight each other in canon games, and they both are relatively introverted individuals with few 'social skills' and a cold class
Well I can say right now that Blaze isn't gonna be in the comic, the main characters have already been listed. But it's probably a good thing she isn't going to show up because I don't think all the readers are ready for my rareships just yet