How LEs are aligned

Let me rephrase that: it doesn't let you easily find anything about your design or the performance.

From the LE placement you would need for each register to find out what it is doing, what part of your code it is accomplishing, what other registers or modules it is connected to, what are the time delays to those modules, and whether those delays are compatible with your requirements or not. It would take ages, and Timequest already does that automatically for you, so why bother?