Apologies in advance if I'm not interpreting your question correctly.
Are you asking about the height of the baffles being affected by sewing opposite sides of the baffle material to their respective shell pieces, causing a vertical "Z" shape? If so, the difference is very minimal, so small that your seam accuracy will cause a much more significant height variation. Also keep in mind that the quilt is a not a rigid structure, and the down decompression and weight (in a hung UQ) will want to pull the baffles straight.
Also a note about darts: When I was talking about them being unnecessary, I was referring to the practice of darting both the inner and outer layers to make an "ovoid" quilt. If you are darting the ends of the wider outer layer to match the width of the inner layer for your end seams, that's a great idea and one that should work very well. I may run some numbers and see if I can make that into an optional addition to the calculator.
I was asking about that indeed!! I figured it wouldnt affect it that much, but me being completely rediculous in my planning and end product, I had to ask. let me know about that dart idea, I have to make another UQ down the road, so I might try and complicate it more!!
"Some ships are designed to sink… others require our assistance."