Watching the announcement at Space X I was confused about the new engine arrangement. All the nozzles look the same size. Is there still a mixture of vacuum engines and sea level engines? Or did they choose one or the other, or maybe optimized for a compromised mid altitude?
In order to minimize the development risk and cost we decided to commonize the engine between the booster and the ship. A future upgrade path for BFS would be to have a vacuum-optimized nozzle.
Where you see that cargo around the perimeter, you can actually switch out those cargo sections for a vacuum-nozzle version of Raptor.
We can do the 100 tons to the surface of Mars with those engines. But version 2 would have the vacuum engines most likely in place of those cargo racks.
There is no compromise. Those are simply the booster engines. Even with those engines, they will be able to fulfill their goal of 100 tons to the surface of Mars. Removing some of those cargo racks later on and replacing them with vacuum Raptors will then improve on that even further, with better fuel economy meaning smaller tanks (or just less fuel) which "buy back" the loss of those cargo racks.
The reason for this is to minimize the number of variables and standardize as many parts as possible, which will minimize risk, costs, and development efforts.
The engines are all now sea level engines, they removed the vacuum ones from version 1.0 to reduce complexity. They did arrange things such that they can add in more engines if required for the future. The bottom area near the engine nozzles now is for storage.
The bonus cargo capacity that two different engine types would allow wasn't worth the extra development time, money, and complexity for the initial version. It's designed that in later versions vacuum-optimized engines can be added.