I want to buy a premium 7-seater within a ₹40–45 lakh budget. My shortlisted cars are the Jeep Meridian, Toyota Fortuner, Skoda Kodiaq and MG Gloster. I’ve heard reliability concerns about the Meridian and Gloster. The Kodiaq’s AC performance is reportedly weak, and the Fortuner’s ride quality is said to be poor. Given these issues, which one should I choose?

You have correctly identified each SUV's weakness; thus, it really boils down to which of these is the least worry for you. On the whole, the Skoda Kodiaq is something you could consider, unlike the other car's weaknesses. 
Also, you could offset the lower AC performance of the Skoda with good habits like parking the car with a sunshade and also using window blinds.
If you are open to looking at an EV, we would recommend you look at the Ioniq 5. It isn't a three-row vehicle, but it addresses all of the weaknesses you have mentioned in the other cars in your shortlist.