Recording to a polyphonic WAV instead of writing multiple mono WAVs (or two stereo WAVs) won't matter.
Phase won't matter in isolation (each channel played back on its own, all by itself in isolation) but will if:
1) one channel of the pair has reverse polarity in comparison to the other channel (possible but not likely in this case- stereo imaging will also be all wonky, sound will be phasy).
or
2) if the two stereo sources are mixed together and one source has inverted polarity with respect to the other. That's more likely.
Do you hear the lack of low end when listening to the 150 source alone, or only when mixed together with the 461 source?