[Zolda]

There's a crucial point I forgot to include in my post above. The main reason behind Fuga's appearance in episode 40 was because the writers needed to retcon the internal logic about the creation of the Nijigon egg. The writers needed to insert the new revelation about the Philospoher's Stone, which had never been shown, stated, implied, nor hinted at all in previous episodes.

Why Fuga? Well, because so far, Fuga is the only character in this story (besides the Alchemist of Dawn who will perhaps appear suddenly without any prior hints) who knows about Nijigon's past, so his presence in episode 40 (and the subsequent dialogue between him and the protagonists) was crucial for the retcon. Fuga must meet the protagonists (and thus, the viewers) to tell them about the retconned internal logic. Since Houtarou had already got Nijigon, Fuga wasn't needed anymore, so Fuga himself had virtually no reason to meet the protagonists. So, how to make Fuga meet the protagonists? The answer is: By contriving the Unholy Trinity's plan to ambush Fuga's place in episode 40. The Unholy Trinity could've ambushed Fuga, no matter where he hid, without involving Atropos or Clotho. So, why was Atropos involved? The answer is clear: To leak the intel to Rinne so that the protagonists could come at the right moment to save Fuga, and also to create the sub-plot in episode 41. If Atropos wasn't involved, then no one would've leaked the intel to the protagonists, and Fuga could've died as the result. If Fuga died, then there was no one left in the story who had the capacity to tell the protagonists (and thus, the viewers) about the retconned internal logic.

TLDR:
Fuga's appearance in episode 40 was crucial for the retconned internal logic about Nijigon. No Fuga = No retcon.

And also, what was the point of the Unholy Trinity's attempt to attack and kill Fuga in the first place? Whether Fuga was dead or alive, it made no difference to them. There was no strategic advantage gained by the Unholy Trinity from Fuga's death. Their main targets were Nijigon and Houtarou. So, instead of directly going after Nijigon/Houtarou, why did they attack Fuga first? Why did they create a convoluted, meandering plan in episode 40? Well, the answer is because the plot needed it to happen. The writers made them do it because the retcon was crucial. The writers basically manipulated the characters' decisions to create the plot.

Another weird thing in this episode that I forgot to mention is the scene @ 14:41 where Minato was able to know that Germain was heading to the concert venue. How the heck could he know Germain's plan? Did someone (whether Atropos or Clotho or Gigist or Gaelya) from Germain's side leak an intel to Minato? None of that was shown, told, hinted nor implied in this episode. Weird! It would've made more sense if Germain wrecked the concert venue and drove Houtarou to anger. Houtarou's internal psyche could've been the X factor that amplified Rainbow Gotchard's power, which enabled him (who had only 1% of the power of the Philopher's Stone) to defeat Germain (who had 33%). This X factor could've been the only thing that was impossible to predict by Germain/the Unholy Trinity.