I'm pretty sure the fact they colored Kashmir grey - as in "not rated" - means they didn't include the civil liberties and human rights situation in Kashmir in their overall assessment of India. I can only assume they made that choice because the situation regarding "political rights" and "civil liberties" (the two main metrics in the FreedomHouse ranking) is for obvious reasons significantly worse in Tammu and Kashmir than in the rest of India - due to years of pro-independence insurgency, martial law and other tough countermeasures, like the 2019-2021 Kashmir lockdown, so including the particular situation in Indian-controlled Kashmir in the national assessment would negatively skew the result for the whole of India.

As for the rest of your argument: Putin's "United Russia" party also lost some seats in the 2021 election and until recently, some opposition newspapers and radio stations remained in Russia. It seems Putin was in no rush to get rid of this meak remainder of opposition in his country, as long as his grip on power was never realistically in danger. It was probably a useful figleaf to be pointed to when foreign journalists would address the rapid descent towards authoritarianism and the almost total decline of press freedom in Russia.

But cases like Navalny showed that this tolerance of press freedom and opposition organizations in Russia would end immediately once an organization became dangerous to the regime. First they poisoned Navalny and when by a miracle he survived that, they convicted him on some pretense and sentenced him to years in prison.