I have a few comments on the integer case including (I think) a solution for $m=3.$ I won't tackle the second question, although it may be no harder.
I found the notation confusing so let me restate. You have a non-negative matrix $A=[a_{ij}]$ with $n$ rows, $m$ columns, and constant row sum $s.$
Optional motivation: This specifies a particular type of list of $m$ colorings of a set $S$ with $|S|=s,$ each using some or all of a set $\{c_1,c_2,\cdots,c_n\}$ of colors. We wish to either find a list of colorings of this type or show that there is none. If there is such a list of colorings, we will describe it by a matrix with $m$ rows and $s$ columns showing, for each element, the color it gets in each coloring.
The goal is to create an $m\times s$ matrix $C$ whose entries are colors $c_1,c_2,..,c_n$ with these properties:
- $a_{ij}$ is the number of times that row $i$ of $C$ contains the color $c_j$.
- If $a_{pj} \le a_{qj},$ then the columns of $C$ having $c_j$ in position $p$ are a subset of those having $c_j$ in position $q$.
All that really matters is the multi-set of columns of $C$, their order isn't important. Call $A$ realizable if there is such a matrix $C.$ and call $C$ a realization of $A.$
The following condition is necessary for $m=3.$ I think that might be sufficient, at least for $n=3$. That might even be easy to show (or false.)
For each column of $A$, look at the set of numbers which appear there and take the second smallest. The sum of these numbers should be no more than $s.$
A first comment is that we may assume that each column of $A$ has a $0$ entry because $\min_i a_{ij}$ is the number of columns of $C$ with $c_j$ in all $m$ positions.
A second comment is that if $A=A'+A''$ with each of $A'$ and $A''$ realizable, then also $A$ is realizable. If has only one realization then $A$ and $A''$ are either both realizable or neither is.
The first comment is simply the observation that an $A$ with constant columns is easily seen to be feasible in a unique way.
I will now drop down to the case $m=3.$ If the matrix $A$ has a $0$ in each column, it is necessary that the smallest non-negative entries in each column, when added, are no larger than the row sum. This is because if column $j$ of $A$ is $\left(\begin{array}{c}u\\v\\0\end{array}\right)$ with $0<u \le v,$ then there must be $u$ columns in $C$ which have $c_j$ in the first two positions. These must be different than the columns with $c_k$ in two specified positions.
Let me illustrate by using your matrix $$\left(\begin{array}{ccc}
{\color{red}5} & {\color{green}4} & {\color{blue}3}\\
{\color{red}2} & {\color{green}5} & {\color{blue}5}\\
{\color{red}3} & {\color{green}8} & {\color{blue}1}
\end{array}\right)=\left(\begin{array}{ccc}
2 & 4 & 1\\
2 & 4 & 1\\
2 & 4 & 1
\end{array}\right)+\left(\begin{array}{ccc}
3 & 0 & {\mathbf 2}\\
0 & {\mathbf 1} & 4\\
{\mathbf 1} & 4 & 0
\end{array}\right)$$
I want a $3 \times 12$ color matrix. I see that I need $2$ red, $4$ green and $1$ blue column. These are the first $7$ columns in the illustration below.
I have $5$ columns to go. The matrix with row sum $5$ tells me what is required.
Since the highlighted entries add to $2+1+1 \leq 5,$ the original matrix is feasible. I will further break down the second matrix (losing constant row sums, as it happens):
$$\left(\begin{array}{ccc}
3 & 0 & {\mathbf 2}\\
0 & {\mathbf 1} & 4\\
{\mathbf 1} & 4 & 0
\end{array}\right)=\left(\begin{array}{ccc}
1 & 0 & {\mathbf 2}\\
0 & {\mathbf 1} & 2\\
{\mathbf 1} & 1 & 0
\end{array}\right)+\left(\begin{array}{ccc}
2 & 0 & 0\\
0 & 0 & 2\\
0& 3 & 0
\end{array}\right)$$
Looking at the smallest positive entry in each column tells me that that I need one column red on the top and bottom, one green in the middle and bottom and two blue in the top and middle positions. These $4$ columns are distinct. Since I have $5$ columns to play with, this is possible. The illustration below shows the situation at this point. Off to the right are the colors still to be inserted in each row. There is no choice and no problems arise.