The two are not entirely at odds- modern bioengineering and synthetic biology are getting pretty good at designing living systems that actually work as designed, e.g. a cell factory that produces a useful molecule.

Modularity and simplicity do evolve naturally when selection pressures make those properties beneficial- and in such cases engineering is then possible, and engineering analogies make sense.

A few examples that come to mind: DNA, modular assembly line proteins, etc. In such cases there seems to have been a selection pressure for rapid reconfiguration, which favors composable modular systems where one small change can lead to a new functional system - often in a way that follows simple predictable rules. In some cases the systems are not messy at all- and rival the most carefully planned out human designed systems.