When I was first practicing my long arm skills, I bought several tied quilts from the thrift store and simply cut off the ties and quilted by machine. One of them is on our main bed, good thing because the dog we have managed to chew some additional big holes in it and I would have been really made had it been one of my quilts instead of a $5 thrift store find. We've largely broken the dog of his chewing issues but still don't trust a good top on that bed.
Yes, sometimes holes are left, especially if tied with yarn. They will do less damage/be less of an issue of a back that rots out.
And yes, I've just sliced off old binding before too.