Okay, let me pose a hypothetical for you all. Imagine a world where we got a Mallow spirit, but not a Geno spirit. That would make the intent extremely obvious. So of course they wouldn't do that. Omitting Geno and Mallow entirely from the game in preparation for DLC also wouldn't sit well, considering Sakurai's spoken on Geno before.
Similarly, bringing back the Chocobo Hat with Hero would just be incredibly confusing and suspicious if Geno wasn’t there as well.
Honestly, the following is a totally baseless theory, but here’s what I think could’ve happened with Geno and Square:
Brawl Era: “Who the **** is Geno? We own that character? Eh... we’re not really interested.”
4 Era: “Hey, we want to be in Smash now... oh, what’s that? You’re still on about that puppet guy? We can... make him one of those costumes to go along with Cloud, how about that?”
Early Ultimate Era: “...Alright, alright, fine, you can keep Cloud in the base game, but we’ll need new DLC as well. ...Geno? Nah, you can make him one of those Spirit things, let’s go with DQ.”
Late Ultimate Era, after Geno becomes one of the major stars of the Smash hype and speculation scene: “Wait, wait, wait, you’re telling us that people actually want this puppet thing? Seriously? Let’s make a deal, then.”
I 100% believe that if Geno’s happening, it was a very late decision based on renewed popularity from Ultimate hype, where he became an exceedingly common name.