WordPress has put together a solution that works well. This solution is not necessarily better or worse than other platforms, it just has different advantages and disadvantages. When in Rome, it is not necessarily best to do as the Romans do (Rome did fall, after all), but you had better be aware of their modus operandi.
In general, WordPress offers a clean and efficient way to get many sites off the ground. However, its flexibility has allowed some less-experienced developers to create unenviable code patterns that are difficult to maintain and debug, and this is what we are striving to avoid. Above all, we encourage you to strive for clean and concise code while working within this, or any, system.