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Let's say I have two premade PCB footprints with courtyards already defined (either from some tool like a footprint generator, from a vendor, etc). Are courtyards usually defined
You'll have to take a good look at the part itself, compare to any in-house design rules, and maybe ask around to see if there are any unwritten rules you might be violating. Most of the courtyards I've seen are as small as they need to be and I wouldn't be comfortable overlapping them but, especially for mechanical parts, you can get away with thoughtful violations. Some examples I can think of where I had courtyards overlap:
Alternate part footprints for a SMD and THT device.
Connectors that had a big courtyard the width of the whole housing for an area where very narrow leadframes were going into the PCB or sockets that make extremely generous clearances for the mating plug.
Putting small SMD components under the overhang of a large axial lead capacitor.
Beware of e.g.: retention clips that need space to flex or things like that.
On this right angle connector, the plug comes in from the top and is almost flush with the board, so that's a no-go area. It might be tempting to overlap just a bit on the sides to get higher density, but the locking clips need all that space to pop over tabs on the plug, so overlapping there will make the socket unusable. There are however two pretty big chunks where you could drop another part, below MH1 and MH2 on the outside of the pins 2 and 12, respectively.
