LM3 wasn't the only game to miss a spirit event TBH. Mario Maker 2 and Yoshi's Crafted World also lacked one. Whilst the former isn't really based on characters as much, considering they literally had a Labo spirit event, I don't think the lack of characters was an issue for MM2. As for the latter, whilst it is true Crafted World got represented via a skin, you could also argue LM3 got represented with the updated poltergust and grab for Luigi.
With all this in mind, it just seems they had to miss a few games out for spirit events, which isn't exactly surprising since the first spirit event we got was in September 2019 and 2019 in general was packed with new releases anyway.
Now that I think about it, I guess you could argue that MM2 and Yoshi's CF released before September meaning they were kinda old news but since Astral Chain, Ring Fit etc etc all waited like 3 months for a spirit event, I don't see why they couldn't have done the same for MM2 even if it existed beforehand. They likely just had to cut some games that could have warranted representation and LM3 was one of them. Doesn't have to equate to playable King Boo