Regarding your guess: $\mathcal M_1\cup \mathcal M_2$ is not in general a $\sigma$-algebra (unless one contains the other), and even if it is, $\mu_1+\mu_2$ is not defined on all of $\mathcal M_1\cup \mathcal M_2$.
What you can do instead is take $\mathcal M=\mathcal M_1\cap \mathcal M_2$ and $\mu_1|_{\mathcal M}+\mu_2|_{\mathcal M}$. Then you can check that everything works.
However, there is (in my opinion) a better way to see this. Notice that the $\sigma$-algebras you have always contain the Borel $\sigma$-algebra (this is a part of the construction in Rudin's book; besides, for sufficiently simple ($\sigma$-compact) $X$ this is actually necessary in order to integrate all compactly supported continuous functions).
On the other hand, if $\mu$ and $\mu'$ agree on the Borel $\sigma$-algebra (or any $\sigma$-algebra with respect to which all functions in $C_c(X)$ are measurable), then for each $f\in C_c(X)$ you have $\int f\,\mathrm{d}\mu=\int f\,\mathrm d\mu'$, even if there is some (non-Borel) set $A$ for which $\mu,\mu'$ are defined and $\mu(A)\neq \mu'(A)$ (although in this case, they can't both be regular).
Further, if $\mu,\mu'$ are distinct Radon Borel measures (that is, locally finite, inner regular with respect to compact sets), then they necessarily disagree about the measure of some compact set $K$, which can be used to construct some $f\in C_c(X)$ which has different integrals with respect to $\mu,\mu'$.
This can be used to obtain the following statement of the Riesz representation theorem:
If $X$ is a locally compact Hausdorff space, then the space $C_c(X)^*$ (the continuous dual) is naturally isomorphic (as a topological vector space) to the space of all Radon signed (or complex) Borel measures on $X$ (with the corresponding weak topology).
The Borel $\sigma$-algebra can be replaced by the $\sigma$-algebra generated by the preimages of open intervals by continuous functions (which may be strictly smaller), and usually also by a strictly larger one (consisting of the universally measurable sets); this is all equivalent by the regularity hypothesis. You can also replace $C_c(X)$ by its completion $C_0(X)$