I think you guys are misinterpreting the last scene. The time loop is broken. However, the timeline is not. So the entire Wakusei Closet encounter must still happen regardless. It's just that it won't result in another loop this time. The last scene explains how the original encounter started. The way the story was originally set up we thought that Flare was the earlier encounter in the loop, but it wasn't. Aimi's was.
So the real sequence of events was:
Senpai's aunt dies and opens a portal - AIMI ENCOUNTERS THE SNAKE (timeline starts) - Aimi meets Flare - Aimi and Flare meet Pisu - Takasugi dies - Aimi starts trying to get Flare and Nako out - Aimi encounters the tower, the weapon, aliens - Aimi finds senpai's aunt in the real world - Aimi tries to get Flare and Nako out but fails, her hand is left behind and turns into Pisu - Aimi grows up, marries, has Megumi - Aimi dies - Megumi grows up and meets senpai - SENPAI TURNS INTO A PORTAL AND EATS NAKO (point of no return) - MEGUMI IS CUT IN HALF (original timeline end IRL) - FLARE MEETS AIMI (loop starts) - LOOP - LOOP - LOOP - .... - LOOP - LOOP - Aimi figures out it's a loop and tries to break it - LOOP - Aimi meets Megumi earlier, sends Pisu to help - MEGUMI REMEMBERS AND BREAKS THE LOOP, CANCELING THE ORIGINAL END OF TIMELINE.
Everything before the point where senpai turned into a portal must happen for the rest of the story to play out.
So the real sequence of events was:
Senpai's aunt dies and opens a portal - AIMI ENCOUNTERS THE SNAKE (timeline starts) - Aimi meets Flare - Aimi and Flare meet Pisu - Takasugi dies - Aimi starts trying to get Flare and Nako out - Aimi encounters the tower, the weapon, aliens - Aimi finds senpai's aunt in the real world - Aimi tries to get Flare and Nako out but fails, her hand is left behind and turns into Pisu - Aimi grows up, marries, has Megumi - Aimi dies - Megumi grows up and meets senpai - SENPAI TURNS INTO A PORTAL AND EATS NAKO (point of no return) - MEGUMI IS CUT IN HALF (original timeline end IRL) - FLARE MEETS AIMI (loop starts) - LOOP - LOOP - LOOP - .... - LOOP - LOOP - Aimi figures out it's a loop and tries to break it - LOOP - Aimi meets Megumi earlier, sends Pisu to help - MEGUMI REMEMBERS AND BREAKS THE LOOP, CANCELING THE ORIGINAL END OF TIMELINE.
Everything before the point where senpai turned into a portal must happen for the rest of the story to play out.