D-9341 being a former high-level researcher makes it reasonable in-universe that he might be aware of what to avoid and how (even if he was amnesticized, he could still have retained some subconscious "don't do this" instincts), rather than just "the player read the guide and made him not do a thing he might otherwise have seen no reason not to do". And it doesn't contradict the Born Lucky assessment in ending A2, because knowing what is after him doesn't stop it from popping up out of nowhere.
SCP-079 insists that in order to escape, you need to use Gate B. But a player can in fact escape using Gate A. If you do in fact use Gate A, there is no radio chatter about SCP-682 escaping, and no attempt to detonate the Alpha Warheads. SCP-079 is speculated to be in league with SCP-682. The whole reason SCP-079 insists you need to use the Gate B exit is because he already needed to open Gate B to let SCP-682 out anyways.
Gate B1's (Exit through Gate B, leave Warheads on) is quite horrific upon further glance. The Foundation nukes SCP-682 as a last-ditch effort to terminate him, and in the post-ending dialogue it's revealed that 682 survived the blast. It sounds like an option that didn't work, but it gets worse when you think of 682's adapting capabilities. Since he survived the blast, not only did he adapt to the radiation, but he also adapts to the full force of a nuclear weapon, making him an unstoppable monster that can and probably will cause an XK-class end-of-the-world scenario. Nice work Foundation.
