A topology on a set $X$ is a family $\mathcal{T}$ of subsets of $X$, which are open sets and satisfy:
(1) $\emptyset, X \in \mathcal{T}$.
(2) Any union of elements of $\mathcal{T}$ belongs to $\mathcal{T}$.
(3) Any finite intersection of elements of $\mathcal{T}$ belongs to $\mathcal{T}$.
An open set $\mathcal{T}$ is defined as a set such that for every $x \in \mathcal{T}$ there is some open interval $(x-\epsilon,x+\epsilon) \subseteq \mathcal{T}$, with $\epsilon > 0$.
Then by the definition of an open set it is not difficult to argue that:
(4) The union of any family of open sets is open.
(5) Any finite intersection of open sets is open.
Does this mean that conditions (2) and (3) just follows from the fact $\mathcal{T}$ is an open set?
Furthermore, isn't it an assumption of set theory that $\emptyset$ is a subset of any set and thus automatically $\emptyset \in X$?
Your logic is backwards here. The three axioms you give are the axioms defining a general topological space. When you start talking about open intervals, you're talking about the set $\mathbf{R}$ (open intervals don't make sense in a general set). You're specifying a collection of sets of $\mathbf{R}$ that you want to be the opens of a topology, and because, as you observe, the union of any family of such sets, and any finite intersection of such sets, is again such a set, the collection is indeed a topology (well, once you also verify that $\mathbf{R}$ itself and $\emptyset$ satisfy the condition you give involving open intervals).