These only provide a "likeliness" rather than concretely proving that the addresses are connected. Its very much guesswork, and the addresses should probably be monitored to see if send from the same output several times, to increase the likelihood that the addresses are connected. So, although its a good system, and usually is indicative that the addresses are related, it doesn't exactly mean the addresses are connected without a shadow of doubt.
It is really not possible to prove beyond any doubt that two addresses are connected to the same person. There is always the possibility that the person would claim something along the lines of that they sometimes sign transactions with another party for whatever reason.
I think the OP is probably trying to create a tool similar to walletexplorer.com (there are several that sell their services). Anyone developing this kind of tool will need to strike a balance between what level of certainty they want to have and the number of false negatives (saying that two addresses are
not connected to the same person when they are) they are comfortable with.