Answer: The difference between a manual brake and power brake pedal housing is in the the mounting flange at the firewall.
Power brake boosters have threaded studs that protrude through the firewall and housing flange and are held on by 9/16″ nuts. Manual brake master cylinders use bolts that protrude through the firewall and screw into a threaded insert in the brake housing.
Housings that do not have the threaded inserts on the firewall flange are for power brakes. Housings that do have these threaded inserts are for manual brake applications.
As far as the MT vs AT, for a 1969 Mustang, there is usually not any difference between manual and automatic transmission housings. Sometimes there is a bolt-on clutch spring hook (depending on the Mustang year). The factory punched the same mounting holes in all of the Classic Mustang housings.
The longer power brake pedal does not swing from the same pivot point that a manual brake or clutch pedal swings from. The long power brake pedal swings from a bolt at the very top of the housing. All housings also have these holes.