"The instances cited by the government took place before X was acquired by billionaire Elon Musk in 2022. Under Musk's leadership, the company has complied with takedown orders."
Twitter refused pre-Musk, X doesn't seem to have a problem doing what Modi says as far as I can tell.
Continuing a lawsuit is not the same as agreeing with the initial claim.
Sometimes, new leadership of a company continues lawsuits because stopping them will incur a huge penalty (in fines, restrictions, control, ...). But that does not mean they will have it started to begin with.
The article is from September 2023, like a year after Musk's takeover of Twitter, and it talks about Twitter not complying with the Indian govt orders in 2023.