I have a top load machine and have made a fair number of rag quilts.
I set the machine to presoak, it does not drain on this cycle. Once the cycle is complete I run a strainer through the of the water to remove as much of the thread scraps as possible. I reset the cycle to the beginning to let it agitate some more and repeat. I do this 3-4 times in total. It may seem like overkill, but I get a huge amount of thread scraps. Then when I put it into he dryer, I clean the lint trap several times.
I would not wash a rag quilt at home if we had a septic tank. I cannot imagine the harm all that lint would cause.