What you’re describing is actually expected behavior. When wow and flutter are enabled, they introduce a vibrato-like modulation. Blending that with a dry signal using the mix knob creates a classic chorus effect — that’s exactly what it’s meant to do. So in this case, the “phasing” you’re hearing is the intended result of those controls working together.
The note in the documentation about the mix knob “avoiding phase issues” is more relevant when wow, flutter, and dropouts are turned off. In those cases, the mix knob is designed to preserve clarity and avoid comb filtering, so you can dial in parallel drive or compression without the EQ getting weird. Think of it more as a tonal design choice for clean signals, rather than something meant to counteract modulation effects.
Hope that clears it up!