No, I think the problem here is that you haven't read the indictment. That automated process was the primary (and, according to emails subpoenaed in the investigation, apparently the only) means of issuing notices and takedowns. Schmitz at one point instructed an employee specifically not to honor takedown requests made outside that process.

"We have a funny business... modern days pirates", said one Mega- employee to another. "We're not pirates", he responded. "We're just providing shipping services to pirates."