Folks,
The confusion is common and has been so for aeons. If I may be permitted to add to cosmo kramer's observations, above ..
The Certification Standards (eg FAR25) are concerned with providing a vehicle which is reasonable to fly and repeatably so. Indeed, one could say that one FAR25 Type is much the same as another for aircraft in recent decades and that is the intent of the Standards and certification processes.
This is addressed without any particular concern about runways and rocky bits.
What you do with the vehicle once you get your hands on it is a whole different ball game.
Then, for obstacle considerations, it becomes an ops engineering concern.
At the end of the day the Certification Standards (eg approach and landing climb WAT limits) conspire to constrain the MTOW and MLW without any consideration being given to the runway and airport environs.
If the runway or obstacle situation dictates, then the AFM limiting weight must be reduced further to accommodate whatever ends up being the critical case for the particular operation.