I drive about 300 km weekly on the highway and 150–200 km in the city. I need a car with better mileage than the Ignis, good comfort, strong safety, and ample boot space. I’m open to CNG but not electric. My budget is ₹10-12 lakh. What do you advise?

The CNG Hyundai Exter would be a good option for you. The CNG setup consists of dual tanks that fit under the boot floor, thus you will still have a usable boot. 

The seats are a bit firm, and the cabin is narrow, so if space and comfort are also very important, you can look at the Tata Nexon CNG. It too has a dual CNG setup below the boot floor, and the cabin is roomier than the Exter. The ride too is comfy and well composed at highway speeds.