Let $S$ be a base set of size $n$. Also denote $k$ of $S$'s subsets by $A_1,...,A_k\in 2^S$ such that $\bigcup_i A_i=S$. Furthermore, let $n_\alpha=\lvert\bigcap_{i\in\alpha}A_i\rvert$ be the size of the intersection of sets in the index set $\alpha\subset I=\{1,...,k\}$. For example, $n_{1,3,4}=\lvert A_1\cap A_3\cap A_4\rvert$ if $k\ge4$.
We know that $\forall i\in I: n_i\ge3$ and $\sum_i n_i>\sum_{\alpha\subset I} (-1)^{\lvert\alpha\rvert+1}{n_\alpha\choose2}$.
If I could show that $\sum_{\alpha\subset I} (-1)^{\lvert\alpha\rvert+1}n_\alpha\le2k$, that would help me a lot with my project.
I have tried an inductive proof but got stuck. I have also tried to represent the task with two lattices (or semi-lattices, I am not sure) and find some mapping there but that failed too. I have checked Richard Stanley's book on Enumerative Combinatorics but I did not see anything that would connect inclusion-exclusion sums of numbers and binomial coefficients.
I would be very grateful for any ideas. Thank you.
We will adopt the convention that the empty intersection $\bigcap_{i\in\varnothing} A_i$ is $S$ (which is natural because $S$ is the identity of the intersection operator on the algebra of sets over $S$.) Also, we will use the indicator function notation
$$ \mathbf{1}_A (x) = \begin{cases} 1, & x \in A, \\ 0, & x \notin A. \end{cases} $$
This is convenient, because for each $\alpha \subseteq I$ we have
$$ n_{\alpha} = \left| \bigcap_{i \in \alpha} A_i \right| = \sum_{x\in S} \mathbf{1}_{\bigcap_{i \in \alpha} A_i}(x) = \sum_{x\in S} \prod_{i\in\alpha} \mathbf{1}_{A_i}(x). $$
Then
\begin{align*} \sum_{\alpha \subseteq I} (-1)^{|\alpha|+1} n_{\alpha} &= \sum_{\alpha \subseteq I} (-1)^{|\alpha|+1} \sum_{x\in S} \prod_{i\in\alpha} \mathbf{1}_{A_i}(x) \\ &= - \sum_{x\in S} \sum_{\alpha \subseteq I} \prod_{i\in\alpha} \bigl(-\mathbf{1}_{A_i}(x) \bigr) \\ &= - \sum_{x\in S} \prod_{i\in I} \bigl(1-\mathbf{1}_{A_i}(x) \bigr) \\ &= - \sum_{x\in S} \prod_{i\in I} \mathbf{1}_{S \setminus A_i}(x) \\ &= - \sum_{x\in S} \mathbf{1}_{S \setminus \bigcup_{i\in I} A_i}(x) \\ &= - \left| S \setminus {\textstyle \bigcup_{i\in I} A_i} \right|. \end{align*}
Note that this formula is valid for any finite family of subsets $\{A_i\}_{i\in I}$ of $S$. Now, OP's condition tells that $\bigcup_{i\in I} A_i = S$. Therefore, we always have
$$ \sum_{\alpha \subseteq I} (-1)^{|\alpha|+1} n_{\alpha} = 0 $$
regardless of all the other conditions imposed.