When structures are skewed to their headwall, does that affect the wingwall angles at all? Or no because it is just based off of the stream and wingwall?See below drawing. Stream left would be 45 degrees and stream right 0?
You nailed it. Wingwall angle is recorded with respect to the angle between the direction of the stream flow and each wingwall. So in the diagram you included, the stream right wingwall would have an angle of 0 degrees, while stream left would be 45 degrees.
Even though the skew of the headwall makes this difficult to assess, and would make the true effects on the flow hard to determine and probably beyond the capabilities of the models we use, the simplistic answer / guideline is to ignore the slant of the headwall - which is driven by the assumption that in the majority of cases it is perpendicular to the direction of flow, and it is the wingwalls that might be weirdly angled.