Actually, I just checked and it might just be possible that Japan might have less than 3 slots. I thought Iruka won Juniors Worlds last year but it the JGP she actually won. If she did place high in Junior Worlds then the only way Japan wouldn't have 3 slots is if the other skaters totally bombed... which would mean they aren't consistent in the first place.
As for the other skilled Junior skaters... where were they in the JGP then? They can have a Silver and Bronze at best (as any better they would've qualified over Inori or the Italian) and their combined score must be lower than the Italian's to lose the tiebreaker. But the Italian's scores can't be that high given that she doesn't have any golds. Meanwhile, Inori's gold was over an American who took gold in another event.
Inori was picked as a designated skater B. That alone means Japan thinks she's in the top 10 Juniors at least. She's the only one among them (aside from Iruka) who managed to win an international tournament this year. Simply put it seems that this batch of Juniors seems to have shit the bed aside from Inori and Iruka. You'll even note that the Designated skater B featured in volume 5 actually aged into senior as Inori entered Juniors, so it seems that this batch of Juniors is sparse.
Your theory is...quite benefit to Inori. You assume that good skaters have gone up to senior already. But as I said before, the author didn't introduce many skaters in Junior field. The 3 girls we saw in volume 5 is 3 famous skaters coming from Chubu block, and Japan has 6 blocks like that. Although all blocks can't have designated skaters, but there's no one say there's only 2 designated skaters in Junior field in volume 5.
Did you see how tough it is in Kinki block last year? (where we have Suzu and Ema in).Ema scored 80 but she got 7th place, but if she was in Chubu block, she could get 2nd or 3rd place and enter Novice All Japan. My assumption is: the level of skaters in seven events in grand prix series are different. In easier event, you can win by scoring 100, in harder event, you have to score 130 to win the game. And finally, both of them secure the same 15 points. You can't say this skater is better than that skater because she places higher than others in different events. We have to check their actual score to judge.
This is how it works. And this is why All Japan exists. To gather up all Japanese skaters for judging. You should have high placement in All Japan to be chosen to go to international competitions. And I 100% sure that many Junior skaters place higher than Inori in this year.
Ah, I have to add that there's no problem for me if Inori is sent to Junior Worlds, only if the author can have a reasonable explanation ☺️