So sorry to hear about your TB. I had an off the track TB for a number of years and he was a wonderful horse, sometimes too smart for his own good, but a great companion.
The main problem I can see would be for quilts that you are going to use as something other than wall hangings, if the materials in the embroidery are something that can't be laundered in the same way as the rest of the fabric you are using.
I do all my FMQ on a domestic machine using either a "hopping" foot or a ruler foot. I've never had a problem with embroidered stuff interfering with the foot since I can just scoot the quilt around to avoid trouble spots if they occur. I did once have a quilt that had lots of bulk from seam allowances in the areas where some of the blocks came together. In that case I was using my ruler foot and it couldn't clear the corners of some of the blocks, but I was able to get around that problem by raising the needle and foot, then carefully advancing the quilt a little, lowering needle and foot, taking a stitch and repeating that process until past the high spots. This would not have been a problem if I had been using my regular hopping foot.
I think you should try it out and see if you like the result, with the idea that maybe the quilt would need to be used more gently than some others.
Rob