I bought the Janome 11000 when they first came on the market specifically to enhance my quilt making efforts. However, I make only large quilts and found that the weight of the quilt causes design distortion if I hoop and embroider all 3 quilt layers, so now I embroider the blocks first and then assemble the quilts. I have had a FEW designs sew out successfully on all three layers, especially along the border area, but it's pretty "iffey" so I don't make a habit of it. Once I've gone to all the expense in time, money and effort, I do not want to mess up a quilt by having an embroidery design not do right ... removing the stitches of a flawed embroidery design is a nightmare and leaves some permanent damage to the fabric.
Although I have downloaded a lot of free designs, the ones I buy are almost always very dense and elaborate, so they definitely require embroidery first and quilt assembly later. Whether my designs are bought or freely given, I think only of how I can use them on quilts.
I have successfully covered up some quilt boo-boos with machine embroidery, such as a large dragonfly sewn over a fabric flaw. I've also added free-standing lace butterflies tacked down to a quilt, leaving their wings free.