Like a large and growing number of folks, I believe the POST-ASSASSINATION lunchroom encounter between Mr. Oswald, Officer Baker and Mr. Truly is a fabrication designed to rob Mr. Oswald of his alibi.
However, a scenario might suggest itself that would help explain why the lunchroom was chosen as the location for that fictional encounter:
A man dressed as an officer goes through the building several minutes before the motorcade.
His ostensible task: to check that everyone in the building is a legitimate employee.
His real task: to make sure the sixth floor is kept clear for the motorcade.
On his way up to six, he pops his head into the lunchroom on the second floor. Mr. Truly, Mrs. Reid and Mr. Oswald are in there. The 'cop' seeks verification that Mr. Oswald is an employee. He gets it. He heads on up the rear stairway--------but before doing so, he informs those in the lunchroom (as he will inform anyone else he runs into) that the sixth floor is off limits for security reasons.
On six, he finds Mr. Bonnie Ray Williams. He tells him to get off the floor.
When Mr. Jack Dougherty goes up to six, just before the motorcade, he is told the floor is off limits.