But say you are coming back from Mars and want to land on a Moon base or even just dock to a lunar space station. Now you have to brake all the excess interplanetary speed with your engines! And that might be quite a lot, especially if you opted for going faster to reduce the transit time.
But if you are arriving with the same speed at Mars, you can use the atmosphere for aerocapture first without having to brake all that speed with engines. And people might do that for Moon bound trips as well - first do an aerocapture to an excetric Earth orbit using Earths atmosphere and only then adjust the resulting orbit for Moon encounter. That should reduce the raking requirements quite a lot.
For that reason I can imagine future interplanetary ships always having a degree of aerodynamic capability, so they can make use of the atmosphere to slow down when needed. Even if they are not really made to land on a body with atmosphere.
For landing on earth you only need aerobraking and parachutes. For the moon all you need are the retro rockets (we’ve already done it). To send humans to Mars you need retro rockets, a heat shield, and a parachute. The combination of systems makes the whole procedure a lot more complicated and error prone, increasing risk.
[1] http://sicsa.egr.uh.edu/sites/sicsa/files/files/projects/dec...
Still, I think there are definitely cases where atmosphere helps (even if it causes issues elsewhere).
So even if you used propulsive breaking to get captured into orbit of a body with atmosphere for safety reasons, you can still capture into a very eccentric orbit & then carefully use aerobraking (as demonstrated many times at Mars already) to lower and circularize your orbit before landing. And with a bit better aerosurfaces you could even use the atmosphere to tune your orbits inclination as needed.