I do all my quilting on either my PQ 1500s, my PC420PRW or my vintage vx560, so I can only speak to using domestics as sit down quilters, have never used a long arm for quilting. That said, I frequently use scraps to piece the backs of my quilts. Most of the time I have some large areas of the backs that are not pieced as well as areas which use smaller pieced scraps. I’ve never noticed any problem free motion quilting over the areas where I used the smaller pieces of scraps in the back while Fmq as long as the foot will go over those areas. Hopping feet have worked just fine, but when using a floating ruler foot, then sometimes the foot will need to be temporarily adjusted higher in order to clear bulkier spots. Some ruler feet have a thumb screw mounted on the foot itself that makes the height adjustment quick and easy, others need to be adjusted by loosening the screw that holds the foot onto the machine moving the foot up a little and then retightening the screw, then repeating the process once the foot has cleared that area, which is time consuming and gets tedious.
If you’re using a walking foot to quilt, it would depend on your machine’s ability to feed thick fabric. You might need to “give it a hand “ when going over thicker areas where multiple seams come together in both the front and the back.
As long as your machine isn’t snagging over the seams and you are using a strong needle like a topstitch needle you should be fine as far as needle breakage goes.
Rob