So to be upfront, I am a believer of the number theory and don't really like Yamato, so personally at face value I thought his fruit flat out confirmed he wouldn't be joining. But I'm not close minded, and I have come up with an idea that I think has a solid chance of maybe being the solution.
First of all, I have to say I don't actually know for sure if this is accurate since I don't know Japanese, but I do remember one of the previously posted lists of possible 2.9 names said Fuko fit and means Wolf. So what if the Inu Inu Model Ooguchi no Makami name is there to throw us off, to make people who believe the number theory think Yamato is definitely not joining, but then we get a scene where the fruit is nicknamed the "Fuko Fuko Fruit"?
This could also solve the "guardian deity" issue as well, that could be how the scene plays out. During the wrap up of the arc Yamato decides he can't join because he has to stay as a guardian deity, but then Momo/Kinemon says "What are you talking about? Its jusy the Fuko Fuko Fruit, there's nothing holding you back from having an adventure." Yes that's a super crappy example, just something like that.
As a believer of the theory, I'm not so precious about it that I'm against a loophole like this, and I think it would be a potentially clever way of for Oda to hold to the numbers without making it obvious.