You're correct, most CFD is overkill. Most engineers are not taught when a tool is overkill -- they're just taught to use the 'best' tool they have.
CFD produces pretty pictures that can give insight into a flow -- which can sometimes help diagnose and fix problems with the flow. Beyond that, it often boils down to a smaller set of numbers that are calculated. As you pointed out, lift and drag coefficients are two important ones. CFD will calculate all six major coefficients -- three forces and three moments. All six are worth having. CFD can also calculate the load distribution across the wing, which is important to feed over to the structures folks. Of course, these things can be calculated with much simpler methods.
Most aircraft operate at quite high Reynolds numbers. The boundary layers are relatively thin, and the pressure distribution around the aircraft can be treated as inviscid. A panel code, or even a vortex lattice calculation will do a good job at estimating the six forces and moments (and load distributions) except for viscous contributions to drag, stall, and transonic effects. An Euler code will be able to handle transonic effects and other complexities of compressible flow.
Basic viscous drag can be estimated with a wetted area / form factor buildup. This won't tell you details of where problems occur, but it will get you a very close approximation of the cruise drag.
All of these are approximations, a good engineer understands them and uses good judgement to know when to use which tool. CFD is not only an approximation because of the mesh resolution and the simplification of turbulence. But most CFD geometry models leave out a lot of details of the aircraft -- finite trailing edge angles, gaps and seams, fasteners, antennae and other protuberances, flap tracks, control surface hinges, bonding straps, etc. etc. To capture these things, the geometry model would be much more complex, the meshing effort would surely double, the mesh size would probably double, and the computation time would increase accordingly.
Most CFD is run with control surfaces un-deflected. This means the aircraft is not trimmed in pitch. Most CFD is run without propulsion effects of the engines -- the aircraft is not trimmed in Thrust/Drag and the effect of the giant vacuum cleaner is ignored.
To get around these limitations, you need to run a bunch of CFD cases -- say at a bunch of angles of attack and with a few control surface deflections. Then, you can do some offline calculations to approximate what the drag of the trimmed solution would be if you were to run it. Likewise, you end up doing a handbook base drag buildup to add in the drag of all the things you left out of the CFD model.
That is just for an ordinary cruising aircraft. For complex models like an eVTOL aircraft with many rotors that possibly tilt as it goes through transition -- trim is a complex 6DOF problem and there are many redundant control effectors. You're interested in many angles of attack and climb angles at many velocities through transition. This flow is inherently unsteady and CFD calculations take a very long time. In the end, a single CFD solution is nearly useless -- to get something useful, you need hundreds of such solutions.
Again, this is where lower fidelity tools (some of which can trim on the fly) really shine.
There are times when CFD is essential, but often it is over-used. Master the spectrum of tools and you'll be way ahead.