I think it depends on the type/thickness of batting that you are going to use. If you use too thick of a batting, when you stipple around it you may get a lot of puckering around the embroidery. A thinner bat won't have the same effect. Try doing a sample block first and see what combination gives you the result you are looking for.
I would stipple first before embroidery, I always do all mine this way...wendy
Will be nice when done.
It sounds like it is going to be an awesome quilt. If it were me I would wait until I have all the blocks completed and then decide. Some batting doesn't need lots of close stitching to hold together where as some others need lots of close stitching. The one I use only needs to have stitching every 10-15cm, so I find it good for quilts when I do echo quilting or stitch in the ditch.
I like the sound of your quilt would like to see it finished. If it was my quilt I would not stipple the crazy patch. I would also stipple the blocks first before the steam punk designs.maybe a sample of the two blocks together would be an idea.
I am going to stipple the embroidered blocks last because I don't want all of the embroidery coming through all of the layers.