Let $s=|S|$.
We show that the question boils down to deciding whether a given $n$$s$-uniform hypergraph admits a panchromatic coloring (when all colors are present in every edge) in $n$$s$ colors. Moreover, the two questions are in fact equivalent, so a good criterion for them exists or not simultaneously. (Seems that such crterion is unknown.)
This may be a dual setup to that in Aaron Meyerowitz’s answer. We also treat the integer case; the general one seems to be easily reducible to it.
1. First of all, we rephrase the nestedness condition. Fix a $j$ and consider a collection of all the $P_j^i$. This collection is nested, so one may enumerate the elements of the largest of them as $x_j^1, \dots, x_j^{k_j}$ so that each set $P_j^i$ consists of some prefix of that list; i.e., if $|P_j^i|=a_{ij}$, then $$ P_j^i=\left\{x_j^t\colon t\leq a_{ij}\right\}. $$
2. Now, given an (integer nonnegative) matrix $A$ whose row sums are all equal to $n$$s$, we construct an $n$$s$-uniform hypergraph $(V,E)$ as follows.
For every column $j$, we find the maximal number $$ k_j=\max_i a_{ij} $$ in it, and introduce $k_j$ vertices $v_j^1,\dots, v_j^{k_j}$.
For every row $i$, we introduce an edge $$ e_i=\left\{v_j^t\colon 1\leq i\leq n, \; t\leq a_{ij}\right\}. $$$$ e_i=\left\{v_j^t\colon 1\leq j\leq n, \; t\leq a_{ij}\right\}. $$
So, if the matrix $A$ correspond to a nested system of partitions, then the vertex $v_j^t$ is in $e_i$ iff the element $x_j^t$ introduced above lies in $P_j^i$. THisThis means that, in this case, the constructed hypergraph admits a panchromatic coloring in $n$$s$ colors, whih are the elements of $S$.
Vice versa, if such coloring exists, one can merge all vertices having the same color in one vertex, thus obtaining an $n$$s$-element set with desired partitions.
THus we are really interested whether the constructed $n$$s$-uniform gypergraph admits a panchromatic coloring in $n$$s$ colors.
3. Finally, notice that we can obtain any $n$$s$-uniform hypergraph by the procedure above, even while considering only 0-1 matrices $A$. Thus the two questions are really equivalent.
Remark. We can go further, introducing a graph on the same set of vertices and drawing an edge $(x,y)$ whenever $x$ and $y$ lie in one hyper-edge constructed above. Then we are interested in a proper coloring of the obtained graph in $s$ colors. (However, now not every graph can be obtained in this way, since this graph is a union of several cliques of size $s$.)