Let $U = \{u_1, u_2, \ldots , u_m \}$ where each $u_i$ is an $r$-subset of $[n]$ and $\,\bigcup u_i \!=\! [n]$. Construct the intersection graph of $U$. That is, let node $i$ correspond to $u_i$ and add edge $(i,j)$ if $u_i \cap u_j \neq \emptyset$. For example, suppose $n=8$ and $U = \{123, 124, 234, 567, 568\}$. The intersection graph is
$\qquad \qquad \qquad \qquad \qquad \qquad \quad $ 
We notice there are two connected components, ie. $\mathcal{C}(U)=2$. Given $n,r,m$ how many sets have exactly $c$ connected components?
$$ \begin{array}{ll} T_{n,r,m}(c) &= \displaystyle \left[x^c\right] \sum_{\left|U\right| = m} x^{\mathcal{C}(U)} \\ &= \displaystyle \left[y^m x^c\right] \sum_U y^{\left|U\right|} x^{\mathcal{C}(U)} \end{array} $$
Can we come up with an expression for $T_{n,r,m}(c)$ or at least some way to efficiently compute it? I would be happy with an algorithm where $n \le 50, r \le 10$ is tractable. I've enumerated all the nonzero values for $n\le6$ to use for verification.
I've posted a partial answer that reduces the problem to counting $T_{n,r,m}(1)$, the sets with a fully connected graph.
New Notations: Always fix $r$. Suppose $L=(c_1, c_2, \ldots, c_l)$ is a list of non-decreasing natural numbers. Denote by $|L|$ ($=l$) the length of the list and $\sum L = c_1 + \ldots + c_l$ the sum of entries in $L$. Let $T(n, L)$ count the number of sets $U = \{u_1, \ldots, u_{m}\}$, where $m=\sum L$, each $u_i$ is an $r$-subset of $[n]$ and $\cup U = [n]$, whose intersection graph have exactly $l$ connected components with sizes $c_1, c_2, \ldots, c_l$.
Relation with the Old Notation: $$T_{n,m}(c)=\sum_{|L| = c, \sum{L}=m}T(n, L).$$
Inductive Property:
Boundary Condition: $T(n, L)=0$ if $n < r$ or $n > r|L|$.
Restriction Formula: Note that the total number of sets $U = \{u_1, \ldots, u_m\}$ each $u_i$ is an $r$-subset of $[n]$ is equal to $${{n\choose r}\choose m}.$$ On the other hand, one can count it using $T_{n,m}(c)$ according to $\cup U$. We get the total number of $U$ is equal to $$\sum_{n_0\leq n}{n\choose n_0}\sum_cT_{n_0, m}(c) = \sum_{n_0\leq n}{n\choose n_0}\sum_l\sum_{|L| = l, \sum{L}=m}T(n_0, L).$$ Therefore we have $$\sum_{n_0\leq n}{n\choose n_0}\sum_l\sum_{|L| = l, \sum{L}=m}T(n_0, L) = {{n\choose r}\choose m}.$$ We rewrite it as $$T(n,(m)) = {{n\choose r}\choose m} - \sum_{n_0 < n}{n\choose n_0}\sum_l\sum_{|L| = l, \sum{L}=m}T(n_0, L) - \sum_{l>1}\sum_{|L| = l, \sum{L}=m}T(n, L)$$
Punch Line: Define $(n_0, L_0) < (n, L)$ if $n_0 < n$ or $n_0 = n$ but $|L_0| > |L|$. Clearly, one can use the inductive properties, the boundary condition and the restriction formula to compute $T(n,L)$ once $T(n_0,L_0)$ are given for all $(n_0, L_0)< (n,L)$ (call $(n,L)$ complexity of $T(n,L)$) since in all formulas involved the complexity on the right hand side is always less than the complexity on the left hand side.
Update: For computational reasons (as OP mentioned in the comment), one may want to replace the inductive property 2 by a simpler recursion $$T(n,(c)^l)=\sum_{k}{n-1\choose k-1}T(k,(c))T(n-k,(c)^{l-1}).$$ Again the idea in the inductive properties is indeed based on OP's answer.