I never heard there's a difference: factory-reset is factory-reset (which is why both methods are often mentioned alternatively to each other: if you still can power up your device manually, you can use the corresponding item in the Settings menu -- otherwise, you can go via the recovery-mode).
Usually, the menu item in Settings says something like "Reset to factory defaults", while the corresponding entry in recovery says "Wipe data and caches".
Now, what is a factory-reset, in technical terms? Resetting all settings to the defaults of the currently installed ROM, while deleting all data and user-installed apps.
How is that done? By...
/data (user-apps and data, plus Dalvik Cache) and
/cache (app cache)
Now comes the circular reasoning: Isn't that what the corresponding entry in recovery says -- "wiping data and caches"?