Because the truth mustn't get out. Without spoiling other routes, I just finished Flynn's route as my last and I have my own theory as to why certain things happened, keeping things in the realms of solely this route. It definitely is the most confusing route without the proper prior knowledge (still is when you've played through everything lol), so I hope to be clear when I try for an explanation:
1. Why Chase condemned Flynn: You can see that there is this "voice" in Chase's head (by the different font), that feels like a completely different person. You will learn more about this the more you play. Keeping with the whole "the truth mustn't get out" theme, this voice/entity sees that TJ was about to tell the truth to everyone, hence, it takes over Chase and seizes an opportunity to distract everyone and shift their focus to Flynn as it condemns him. This is why Chase acted so out of character in that scene when he's been nothing but horny back to Flynn the past days, because it wasn't Chase.
2. Why Daxton & Carl were there: If you remember the detail there wasn't a gate around the real Smoke Room (which Flynn points out explicitly), This is him entering the mine, because the mine DID have a gate (more like rebar but whatever), and it was actually on fire even before the hysteria. Daxton and Carl follows Flynn into the mine to try to get him out, but simultaneously Flynn is having this creepy conversation with Sydney (again, getting really into it). Seeing the worsening condition of the heat inside, and then Flynn suddenly screaming at them both, they abandon him in fear of their own lives.
My ending explanation: Flynn wanted the truth, then the entity let him see the literal entire truth, every single killing/murder in Echo in brief flashes, from the fox hanging, to Brian's van, and finally Syd, and probably many more that they "all blur together". Yet, he doesn't even see who killed Sydney as his eyes pop. The truth mustn't get out, after all, as the entity toys with him and wins. In the final scene, in Jenna's closet, young Jenna asks if he is real. Flynn, having spent the entire route finding the truth and finally seeing it, denies both its existence, and even himself, as he had destroyed himself in his search for the truth, both physically and mentally, in pure disbelief and regret.