I’d have to disagree a bit on one point here.
The first Sila of Pancasila, “Ketuhanan yang maha esa,” means that we recognize that a being higher than us exists. ‘Ketuhanan’ refers to any being with ‘God’-like aspects, so even though the government only officially recognizes the 6 religions in the constitution(because they’re the overwhelming majority), all other religions which believes in God/Gods is recognized in Indo, not just the monotheistic ones. Of course, in practice it might be different like you said, but it’s not contradictory and all beliefs are recognized in UUD 1945.
This also means that atheists are not acknowledged even when discriminated against, and it’s hard to argue against that(though it’s not the primary issue here) since it’s based on the first and foremost sila of our most fundamental Pancasila, which our nation is built upon.
Still you’re right, democracy is not just majority rules and the Islam can’t just step over the minorities, and it’s crazy how little have changed since 1998.