I think you've gotten some good ideas here. The large zigzagging that bessiecrocker mentions was one of my first thoughts. It wouldn't have to be really wide if you think that might show a lot. I would test a little bit and see what "disappears" into the layers the best.
As Bunnykins notes, you don't need to put right sides together as for a 'normal' seam in this case. Treat it as you would lace, and just lap one edge over the other and stitch that way. You could lap one skirt layer one way and the next the other, but that might not be necessary either.
I'm reading your post again and I see I missed your actual point. I guess staggering the seam position might be a good idea, but if you already have them all attached to the ribbon waistband, how are you going to do that? As for the tacking together of the layers, I don't know that it's necessary, but you get to decide, and if so, I don't think you'd have to do it too often, and maybe not at all for the top couple of layers. Perhaps you could scatter small embroidered motifs or pearls or ribbon bows or something on the skirt and use those points as your tacking spots? Are you having a sash on the dress that could have tie ends to camouflage any 'ugly seam' if it seems to be a problem? I wonder if you could have a very large overlap with your top layer or two and then not seam those at all, and it would cover anything else?
No actual answers, but several ideas anyway, and I hope this helps.
I hope you can attach your photo example so we can see it. Sounds like it's going to be a lovely dress!