The engineering comes from the mathematics.
Engineering is applied physics. Not just mathematics. Mathematics deliver the tools, but physics the relations that you have to work with.
The rocket equation is one important function for spacecraft design, but not the only equation at all. The problem is not the mathematical model, but the engineering reality. On the paper, you can use ideal fuel tanks, that contain the fuel by magic. In reality, it wouldn't work. You have to use real materials, with real qualities, with real errors that are introduced during manufacturing, assembly and flight. And even that isn't the whole truth. You need to get the propellants to the engines with pipes, that have their own physics behind them to work in a way that does not limit your theoretically possible performance too much. Ignore the physics and you get such disasters as the N-1 rocket, that had fuel lines burst by the pressure transients that are introduced when 6 main fuel valves close at the same time, suddenly stopping the fuel flow.
Explanation for those who rarely read physics books: In a pipe, total pressure as the sum of static and dynamic pressure has to be constant. Dynamic pressure is practically the inertia of the flowing medium. When you increase dynamic pressure by increasing the flow speed, the static pressure has to drop. When you stop the flow completely, static pressure is equal to dynamic pressure. When you have a dense kerosene fuel flowing through a pipe every second at 50 m/s, you have a dynamic pressure of about 0.5 * 1000 * 2500 = 1,250,000 Pa or 12 bar. That is quite a lot of pressure, that does usually not act on the walls of the pipe since the flow is parallel to the pipe walls. But when you stop it, the suddenly higher static pressure acts in every direction the same, from the valve to the pipe walls to back into the propellant tank. The flow bounces back from the closed valve and during this short moment in which the flow is slowed, you have a much higher pressure on every part in the system, as during ignition or flight. In case of the N-1, it was too much for the pipes and they burst at their weak spots (eg, welds)
The moral of the long story: Never assume that something works, until you tested it with real materials.
And that is why engineering is more than just a single equation. The equations are not as important for an engineer as knowing which equations he needs to consider in a scenario to get correct predictions.