Here's an outline of the proof in a few steps.
Let $N_\alpha,N_\beta$ be the closed regular neighborhoods of $\alpha$ and $\beta$ on which the twist maps are defined. We also have chosen orientation preserving homeomorphisms $\phi_\alpha : A \to N_\alpha$ and $\phi_\beta : A \to N_\beta$ with $A = \mathbb S^1 \times [0,1]$.
First, we can assume that $N_\alpha=N_\beta$, for the following reason. Knowing that $\alpha$ and $\beta$ are isotopic, it follows that their regular neighborhoods $N_\alpha$ and $N_\beta$ are "ambient" isotopic, which means that there exists a continuous function $h : S \times [0,1] \to S$ such that each map $h_t(x)=h(x,t)$ is a homeomorphism, $h(x,0)=x$, and $h(N_\alpha,1)=N_\beta$. The formula
$$h_t^{-1} \circ T_\beta \circ h_t
$$
then defines an isotopy from
$$T_\beta = h_0^{-1} T_\beta h_0
$$
to a Dehn twist around $\alpha$ denoted
$$T'_\alpha = h_1^{-1} T_\beta h_1
$$
and we conclude that $T'_\alpha$ has the exact same twist neighborhood $N_\alpha$ as $T_\alpha$. In summary: we can use an ambient isotopy from $\alpha$ to $\beta$ to conjugate $T_\beta$ to $T'_\alpha$.
Furthermore, although we don't yet have $\phi_\alpha=\phi_\beta$, and so $T_\alpha$ and $T'_\alpha$ need not be equal on $N_\alpha$, what we do have already is that $T_\alpha$ and $T'_\alpha$ both restrict to the identity map on $S - \text{interior}(N_\alpha)$, and so both also restrict to the identity map on the boundary of the annulus $N_\alpha$. This is clear for $T_\alpha$, and for $T'_\alpha$ it follows from the formula used above to define $T'_\alpha$, together with the fact that $T_\beta$ restricts to the identity map on $S - \text{interior}(N_\beta)$.
Using $\phi_\alpha : A = \mathbb S^1 \times [0,1] \to N_\alpha$ consider the topological arc $J = \phi_\alpha(p \times [0,1]) \subset N_\alpha$ (pick $p \in S^1$ arbitrarily).
Next, we can assume that $T_\alpha(J)=T'_\alpha(J)$, for the following reasons. We know that arcs $J_\alpha=T_\alpha(J)$ and $J'_\alpha=T'_\alpha(J)$ are isotopic rel endpoints in the annulus $N_\alpha$; this is easiest to see in the universal cover $\mathbb R \times [0,1]$ of $A \approx N_\alpha$, where $J$ lifts to $\tilde p \times [0,1]$, and where $T_\alpha$ and $T'_\alpha$ have lifts each of which is the identity on $\mathbb R \times 0$ and which shifts one unit to the right on $\mathbb R \times 1$. It follows that $J_\alpha$ and $J'_\alpha$ are ambient isotopic in $N_\alpha$, using an ambient isotopy which is the stationary on the boundary of $N_\alpha$. Again, by conjugating using this ambient isotopy, we arrange that $T_\alpha(J)=T_\beta(J)$, and everything is still the identity outside of $\text{interior}(N_\alpha)$.
Next, we can assume that $T_\alpha \mid J = T'_\alpha \mid J$: we use here the fact that two homeomorphisms between two arcs which have the same endpoint values are isotopic; that isotopy can then be extended to an ambient isotopy on the surface which is still the identity outside of $\text{interior}(N_\alpha)$, and again we conjugate using this ambient isotopy.
Finally, represent the annulus $N_\alpha$ as the image of the square $[0,1] \times [0,1]$ by gluing the top to the bottom of the square. The map $T_\alpha^{-1} T'_\alpha$ pulls back to a homeomorphism of this square which is the identity on the boundary, and it remains to show that this homeomorphism is isotopic rel boundary to the identity map on the square. This is just the Alexander trick.