There are some differences in the notation of the article with those used in the original question. This answer is provided within the notation of the article.
Key point: The article states that ${\dot{\vec{\alpha}}}\neq{\vec{\omega}}$ with $\alpha$ correponding to the angle of rotation.
Now we can equate $\dot{\vec{r}}=\vec{\omega}\times \vec{r} $ with $\dot{\vec{r}}={\Omega} \vec{r}$ with $\Omega$ is an antisymetric matrix defined by $\Omega_{ik}=\epsilon_{ijk}\omega_j$. THESE are correct regarding positional changes of the object in terms of its angular velocity.
(I suspect what you are refering to as "lim $\Theta(t_1,t_2)\over t_2-t_1$..." is ACTUALLy $\Omega$ in the article, one reason I have migrated to the article's notation so as not to confuse this object with $\dot{\alpha}$ or $\dot{\Theta} $ in your notation.)
Your question as stated then reads to me "How do we proove THIS OBJECT (i.e. $\Omega$ exists and that it equates to the operation $\omega\times$)."
First of all, it has been defined in terms of the anti-simetric tensor $\epsilon_{ijk} $and the angular velocity $\omega $ ; $\epsilon_{ijk}\omega_j r_k=\vec{\omega}\times\vec{r}$
by definition.
But my intuition is that you are intersted in how to arrive at this object starting from $\alpha$ instead. I believe this is demonstrated sufficiently in the first collum of the article.
To summarize: Letting the orthogonal matrix $S=e^{\vec{\alpha}\times}$, $\vec{r}=S\vec{r_0}$. it follows that
$\dot{\vec{r}}=\dot{S}S^{-1}\vec{r}$. Therefor $\Omega=\dot{S}S^{-1}$.
If $\alpha$ exist, $S$ exists and $\Omega$ may be expressed in term of it. It works from both angles. (Also the derivatives of S given in the article are calculable.)
To put another way equations of the same form have the same solution. On one hand we have $\dot{\vec{r}}=\dot{S}S^{-1}\vec{r}$ on the other we have $\dot{\vec{r}}=\vec{\omega}\times \vec{r} $. Therby it is trival to make the interpretive association $\Omega=\dot{S}S^{-1}$
EDIT: In more explicit fashion
1) We have two items to consider initially.
A) The first is $\dot{\vec{r}}=\vec{\omega}\times \vec{r}$, the time derivitive of the position vector $\vec{r}$ as a function of itself. Let $\Omega$ be the matrix object that fulfills this relation. $\Omega$ BY DEFINITION is $\Omega\equiv \epsilon_{ijk}\omega_j$ where $\omega_j$ are the components of the angular velocity.
B) The second is $\dot{\vec{r}}= f(\vec{\alpha})$ the time derivative of the position vector $\vec{r}$ as a function of the rotational angle vector $\alpha$.
Logical connection:
A=B
Since $\dot{\vec{\alpha}}\neq\omega$, as the article demonstrates, $\dot{\vec{r}(\alpha)}\neq\Omega\vec{r}$. QUESTION: what is the relation beteen these items, and consequently what is $\dot{\alpha}$ and/or $\omega{(\dot{\alpha})}$. HINT: $\omega$ is NOT $\vec{\dot{\alpha}}$. Let see what we find instead.
BY DEFINION of the derivative $\dot{\vec{\alpha}}=$limit a $t_2-t_1=0$of${\alpha(t_2)-\alpha(t_1)\over{t_2-t_1}}$ ...
Letting $S_{lm}\equiv e^{\epsilon_{lmn}\alpha_m}=I_{lm}+\epsilon_{lmn}\alpha_m+(\epsilon_{lmn}\alpha_m)^2+...$, it follows that
$\dot{\vec{r}}(\alpha)=\dot{S}S^{-1}\vec{r}$ (See article)
Therfore,
$\epsilon_{ijk}\omega_j={d\over dt}S_{ia}S^{-1}_{ak}$...provides a proper relation beween $\omega_j$
and $\dot{\alpha}$
One may calculate the terms of $\dot{S}_{ia}$
if they wish. This i the only object involving time derivatives of $\alpha $ at this stage. YOu may write those in terms of the definition of the derivative if you desire. I will use a short hand.
${d\over dt}S_{ia}=\epsilon_{ima}\dot{\alpha_m}+h.c.$
$S^{-1}\rightarrow I+h.c$
So we obain after removing the antisymetric tenor from each side
$\omega_j=\dot{\alpha}_j+h.c.$
QED
I feel the rational for the correct relations is sufficiently demonstrated at this point, but may include a couple of further edits if I'm inclined at some point.
Also please lay down what you explicitly define as $\theta(t_1,t_2)$ in term of the notation of the article. If you can do that, your question is nearly answered.
EDIT: OP has since posted his definition as "Note that what this journal paper calls $\vec{α}(t)$ would in my notation be written as $\vec{θ}(t_0,t)$. The paper discusses the fact that the angular velocity $\vec{ω}(t)$ is not equal to the time derivative of $\vec{α}(t)$. This means that the limit of $\vec{θ}(t_0,t_2)−\vec{θ}(t_0,t_1)\over t_2−t_1$ does not equal..."See edit to original question for rest.
...I thought there was something peculiar at hand :)! Actually (I believe, tell me if you disagree), correctly speaking that $\vec{\alpha}(t,t_0)=\vec{\theta}(t,t_0)$ Can we agree that the meaning of $t_0$ is that an initial condition has been applied? In general,$\vec{\alpha}(t,t_0)\neq \vec{\alpha}(t)$. So your correlation of your notation with that of the article is not quite right!
Properly speaking, the limit of $\vec{θ}(t_0,t2)−\vec{θ}(t0,t1)\over{t2−t1}$ does not equal$ \vec{ω}(t1)$...No it does not. But the limit of $\vec{θ}(t2)−\vec{θ}(t1)\over{t2−t1}$ DOES...indeed.
And $\vec{θ}(t_0,t2)−\vec{θ}(t0,t1) \neq\vec{ \theta}(t_2,t_1)$ But $\vec{θ}(t2)−\vec{θ}(t1)$ IS.