I always embellish last, but I also use buttons as a form of quilting, like tie tacking.
On my t-shirt quilts, I do either FMQ or straight line quilting, depending on the size of the quilt. I don't stitch on the shirts, just the sashing and borders. I then go through and add matching buttons on the t-shirts themselves. It adds stability to the quilt, especially if the t shirt pieces are 12".