I interpret the first example as, if you have a formula that belongs to all formulas in this language, then it is deductible from any formula in this language. I think my explaining might be wrong or else you can just prove every deduction with this.
For the 2nd example, where did the singular P come from in line 1? It isn't part of the two implicit assumptions. How does it use the 1st example?

Your interpretation of the first example is not correct. $\Sigma$ is an arbitrary set of formulas. It contains some formulas but not necessarily all of them. Also $\Sigma\vdash A$ does not mean "$A$ is deducible from any formula in $\Sigma$". It means, "with assumptions $\Sigma$, you can deduce $A$". In the process of the deduction you might use more than one assumptions from $\Sigma$. So it's not "any" but "some".
Having these in mind, the correct interpretation of the first example is "from a set of formulas you can deduce each of the formulas within the set". For example, if $\Sigma=\{A,B\}$, then $A,B\vdash A$ and $A,B\vdash B$.
So, rule $(\epsilon)$ is: If $\phi\in\Sigma$, then $\Sigma\vdash \phi$.
Let's take step by step the second example. Note that while building a proof, some formulas might be added or removed from the assumptions. So, in the beginning of a proof we can take whatever assumptions we want, as long as in the end only those stated at the excerise remain as assumptions. Therefore, in the beginning of a proof, we choose the set of assumptions that is the most convenient for us to end the proof with the desired set of assumptions. In this example, we start with a set of assumptions $\Sigma=\{\phi\to\psi, \psi\to\xi, \phi\}$ and end with the set $\Sigma'=\Sigma\setminus\{\phi\}=\{\phi\to\psi, \psi\to\xi\}$, which is the desired set of assumptions.