aarg:
But... they interact. So you have to be familiar with all the possible interactions to avoid difficulties.
If you set them up to interact they will. If not, most of the modules are pretty independent of each other. Changing the ADMUX register isn't going to screw up any part of Timer2's operation, for example. It's nowhere near as bad as you're worried about.
And what are you afraid is going to happen if you mess up? If your sketch doesn't work properly, change something and load a new one. Registers are in RAM memory, any changes you make are cleared out after a reset so nothing you do will interfere with the bootloader. That level of worry is appropriate for fuses, not registers. Fuses are much harder to change (requiring a programming device) than registers precisely because they are more dangerous.
The bigger concern is if you have two bits of code trying to access the same resource, like if Tone and Servo both try to use Timer2. Then things get screwy. But that's a problem with libraries that hide away their access to the different peripheral resources. If you're setting them up yourself, you know exactly which bit of hardware is devoted to which task, so it won't be a problem.