The car parking analogy does not fit. But if you want to use a similar analogy. Assume there is toll road which allows the first 100 cars. This guy uses his superior tech skills, to get his clients (cars) in the first 100. He charges them a premium.

Now the toll road keepers, arrest him for helping his clients? That I think is wrong. If his clients had complained that he didn't deliver on his promise but charged money, then that could amount to cheating. He didn't do that. He used code he wrote to provide a service to his clients.

Yes I agree, it could be hacky code, and it worked because the website was itself sub optimal. But putting him into prison because the website couldn't be made better (prevent his hack) amounts to bullying to hide the technical incompetence.

You're attacking a strawman here. The issue was that he was making a profit by reselling tickets, not by automating filling forms in a website. The mechanism is not particularly relevant.

By analogy, it is legal to park my car in my own garden, but not legal to park it in my neighbour's garden. If I were to do that, I might expect to be punished for "parking my car".

The article itself mentions this:

Under the Railways Act, all those who help passengers with ticketing are expected to register with the IRCTC as an agent. Does this apply for app creators? The officer reserved his comment.

I think the case depends on how the court interprets that question.

There is a difference between "guilty until proven innocent" and "innocent until proven guilty". In India, the former is how the law-enforcement works for most people while the justice system says the latter. Most people entangled in the slow legal system just want to get out of it even if it means injustice towards themselves. And the laws are so convoluted and in this case he has a behemoth monopoly to fight against.