Sigma, Tamron, and Tokina lenses send a lens code to the body that identifies them as a Canon lens. The camera will apply the focus point info for the lens that it thinks is on the camera. Generally, the third party manufacturers pick a current Canon lens with the same focal length and aperture, but not always. This has caused problems in the past when some Tamron lenses sent a code for a long obsolete Canon lens and ended up causing users problems. Tamron updated the lens code, but I do not know if they repaired in service lenses for free.
There is always a risk of something not working correctly with a third party lens, but Tamron and Tokina have the best track record as far as overall compatability. Newer Sigma lenses work well, but there are a ton of older ones out there that will not work on a Canon DSLR, so beware when buying a used one. For example, older 105mm macros don't work, while the newer ones have a fix.