The power of an engine is that it is a series of closely intertwined parts. Often times, the graphics code and collision code are linked; here's an example. Shoot a bullet in any FPS; the resulting decal is likely created from the collision data, since it's much faster to search than the highly tessellated graphics model.
Or, let's say, I have a melee attack. The specific frame that the attack occurs on is likely decided by the animation data. So that means that we need to run animations on the server, against an invisible skeleton.
Similarly, you might encounter a scenario where a bunch of stuff blows up, and you want 99% of that simulation to be baked offline and not simulated on the client, to ensure that the tower lands exactly where it needs to. So now you need to plug together your physics and animation systems, yadda yadda.
These are not bugs, or necessarily problems. People who suggest we turn all engines into tiny independent toolkits are missing the point. Of course everyone tries to make systems as independent as possible. But there's a bunch of power you can unlock if you have even a small bit of close integration between two systems.
How does one manage complexity? The first is to enable everyone, even artist and designers, to be technical. They're already managing complex topologies, doing sophisticated lighting and shading techniques, and often writing custom Python scripts to help them clean up the massive amount of data. A big thing I've seen from developers out of FAANGs is that they're shocked that "non-programmers" are writing custom scripts and doing programming. Your artists and designers are incredibly technical people who are good at solving problems. Trust them.
Invest in custom tools; any bit of custom tooling to make your life easier will pay off massively. Basically, give your whole staff the ability to debug and fix issues, with custom UIs and logs specifically built for your purpose.
QA staff are undervalued here in the US, but anybody who's worked in games for three months knows what a difference a senior QA makes. They know your game better than anybody else. Watching a good QA go from a blurry cameraphone pic on an angry reddit post somewhere to complete repro steps in less than an hour is nothing short of magic.
