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Flammole was not sensing Model W; this is confirmed in ZX Tunes. The text refers to this revelation as a "giveaway", and Area N's proximity with Area K in the map strongly hints that Flammole was actually sensing Omega (or the Mysterious Rock that would become Model OX).
Weil was a human of pure hatred of Reploids. That sheer will was probably what allowed him to live.
Don't forget that his body was stuck in regenerative armor, that his memories were digitized and that he had fused himself with the core of a space cannon.