First of all, at my old university (where many PhD-theses on ordered spaces (LOTS) have been written), in the first course in general topology the order topology was defined to be the unique topology on $(X,<)$ generated by the subbase of open rays. So the question is moot in that context. Munkres has created a bit of a fuzz (IMO) to define the topology by a base instead: it's less elegant because the base depends on whether $\min(X)$ and/or $\max(X)$ exist or not, which makes that we have to consider cases depending on that in a lot of proofs on ordered spaces. This already starts in the checking that the Munkres standard base is indeed a base for some topology at all. For subbase it's trivial (in university we had no condition on a subbase at all, so there is nothing to check, and otherwise take $x < y$ in $X$ and note that $(-\infty,y) \cup (x,+\infty)=X$ so obeying Munkres' demand that a subbase must cover $X$ (if no such $x,y$ exist, $X$ is a singleton and there is a unique topology on $X$ anyway; we don't consider these trivial spaces).
It's more convenient to start from this subbase and consider directly what the generated base by it, call it $\mathcal{B}_g$, is. (we need nothing more; no lemmas from before etc. just that we have a finite intersection of subbase elements as a member of the generated base)
- If $\min(X)$ exists, all sets of the form $[\min(X),x), x \in X$ are in $\mathcal{B}_g$ as it equals $(-\infty,x)$ by definition.
- If $\max(X)$ exists, all sets of the form $(x,\max(X)], x \in X$ are in $\mathcal{B}_g$ as it equals $(x,+\infty)$ by definition. (both a single subbase element, so a "finite intersection" trivially).
- All open intervals $(x,y), x,y \in X$ are in $\mathcal{B}_g$ as it equals $(-\infty,y) \cap (x,+\infty)$.
So Munkres' base $\mathcal{B}_m \subseteq \mathcal{B}_g$. It follows that the order topology $\mathcal T_<$ (generated by $\mathcal{B}_m$) is a subset of the topology $\mathcal{T}_S$ generated by this subbase. In short $$\mathcal{T}_< \subseteq \mathcal{T}_S\tag{1}$$
On the other hand, if we have a finite intersection $B=\bigcap_{i=1}^n S_i$ of subbase elements ($n \ge 1$) define $$L = \{i \in \{1,2,\ldots,n\}\mid \exists L_i \in X: S_i = (-\infty, L_i)\}$$ the left facing subbase elements ($L=\emptyset$ is possible) and similarly $$R = \{i \in \{1,2,\ldots,n\}\mid \exists R_i \in X: S_i = (R_i, +\infty)\}$$ the right facing subbase elements. Then if $L,R \neq \emptyset$, we have $$B=(\min \{L_i\mid i \in L\},\max\{R_i\mid i \in R\})\in \mathcal{B}_m \subseteq \mathcal{T}_<$$ and if $L=\emptyset$, we have $$B=(\max\{R_i\mid i \in R\}, +\infty) \in \mathcal{T}_<$$ and if $R=\emptyset$, we have $$B=(-\infty, \min \{L_i\mid i \in L\}) \in \mathcal{T}_<$$ (Munkres mentions "nebenbei" that open rays are order open in the text) and hence in all cases $B \in \mathcal{T}_<$ and as $B$ was an arbitrary member of the generating base $\mathcal{B}_g$ for $\mathcal{T}_S$ we have that $$\mathcal{T}_S \subseteq \mathcal T_<\tag{2}$$.
$(1)$ and $(2)$ together give equalities of topologies.
The generated base by the subbase is not always exactly the standard order base as defined by Munkres, because it can contain more: all open rays (which are not in Munkres' base if $\min(X)$ or $\max(X)$ do not exist) are in the generated base always. But they give no extra open sets so it doesn't matter.