Look at the average scene in an MCU movie and see that 90% of it is usually CGI. Extrapolate all those effects across a 120 minute film and add in the price of the top name actors they usually have, and I'm surprised it's only 350 million.
Surprisingly, yes. Filming on location and all the logistics that go along with that can balloon the cost real fast, especially for multiple locations. (Site fees, travel, talent costs, additional security, a separate crew unit, etc) CGI allows you to create different locations through green screen, which majorly cuts down on a lot of the scheduling/logistics. Sometimes green screen will be just a window, other times it will be literally the entire set.
They're starting to use sets where, instead of having greenscreen, the walls are giant LED screens where they display the background. This way the director has complete control of what is going on in the scene in the moment. (also, with greenscreen you can get a weird green reflection on the actors that needs to be corrected for).