It's much harder to manipulate paper votes at scale than voting machines. With paper, people know that the correct vote was recorded (a voting machine could silently change it to something else), and the paper can be protected through a chain of custody with monitors from various groups watching it - and then counted by independent groups.
So the threat model is someone hijacks the firmware in a voting machine to record votes other than what the voter selected, and it's much easier for someone to flip millions of digital bits without being detected than for someone to change the box which is ticked on millions of bits of paper.
So the threat model is someone hijacks the firmware in a voting machine to record votes other than what the voter selected, and it's much easier for someone to flip millions of digital bits without being detected than for someone to change the box which is ticked on millions of bits of paper.