When in other modes than M mode, the camera's metering system shows you the level of incoming light by showing you the combination of exposure time, aperture and amplification (ISO) you need to render a standard exposure, as explained by Wilt above.
I full M mode, you set the combination of time, aperture and ISO. Since the camera can't change any of them, it will instead show how far away from standard exposure you are.
When you spot meter, and lock the exposure at the level metered from some part of the subject, then subsequent meterings will be in reference to that point. +3 implies that what you are aiming at now is three stops (eight times) as bright as the spot you used for reference. Whether +3 renders clipping or not depends on the reference. The camera can be set to underexpose the reference (exposure compensation) even in automatic modes. Thus +3 doesn't have to imply three stops above standard exposure, just three stops above the reference.
Cameras today typically have a dynamic range of above twelve stops, so +3 will not automatically imply clipping.
Canon cameras only lock exposure implicitly when focusing if you use One Shot AF together with evaluative metering. If you think about how evaluative metering works, you quickly realize that this is necessary. But in all other combinations of modes, there's no implicit exposure lock when focusing, regardless of how focusing is initiated.