In the hidden world scene ‘king’ Toothless calls out to the dragons of the hidden world. When the dragons respond next to the Light Furies, we see a Bewilderbeast that looks EXACTLY like Drago’s Bewilderbeast from HTTYD 2. It’s even missing his left tusk. Why is this Bewilderbeast not in charge? How did it end up here? I thought it died in HTTYD 2?
I think HTTYD 2 makes it clear that the Bewilderbeast was not killed, but rather retreated - we see him crawling back into the sea after he loses the loyalty of the other dragons during his confrontation with Toothless. Thus, it's likely that he returned to the Hidden World after that, but not as a king - his humiliation in battle with Toothless either caused him to lose any claim to kingship in the eyes of other dragons, or he himself acknowledged that he wasn't worthy of it and supported the Furies' rule.
When the dragons respond next to the Light Furies, we see a Bewilderbeast that looks EXACTLY like Drago’s Bewilderbeast from HTTYD 2.
That's because it is. Dean Deblois, the director, and multiple other cast and 'in the loop' members confirmed that it was Drago's Bewilderbeast. Once I'm able to find where it's confirmed, I'll edit this post.
Why is this Bewilderbeast not in charge?
Since we know that this is Drago's bewilderbeast, we know that his alpha-status was challenged. This was directly said in HTTYD2.
"He's challenging the alpha!"
"To protect you!"
So the battle ensued and at the end, Toothless had won the fight, making him the alpha. We know this because during the battle, the Bewilderbeast started to lose, and eventually completely lost his dragon army. Toothless had officially won the fight and this made him The King of Dragons. This is why all dragons follow his leadership now. Because he won the fight against an alpha and became the alpha.
So to answer your question of why isn't that bewilderbeast in charge? Because he lost his alpha status to Toothless.
How did it end up here? I thought it died in HTTYD 2?
We see at the end of HTTYD2 that it simply fled into the ocean. There was no indication that it, or even Drago himself, died. However I think we're to assume as much based on HTTYD3 and them talking about Drago's fall. And since you enter the Hidden World by either flying in, or over the waterfall, we can assume that the bewilderbeast swam into the Hidden World (or found another way in that isn't from above the water).