To fix the context, let us clear that we are looking for the number of ways to arrange
- $l$ undistinguishable balls
- into $m$ distinguishable boxes, each provided with $n$ distinguishable compartments
- counting only the arrangements that contain no empty boxes.
As a visual help, let us reproduce an example with $m=2, \, n=3, \, l=3$.

Obviously, the total number of ways to put
the $l=3$ undistinguishable balls (the "ones")
into the $m \cdot n = 6$ distinguishable places is
$$
T(m,n,l) = \left( \begin{gathered}
m\,n \\
l \\
\end{gathered} \right) = 20
$$
and deducting the first and last row, in which at least a box is totally empty, we get
$18$ dispositions leaving no empty box, as correctly returned by the $C(m,n,l)$ formula.
That premised, there are various combinatorical and algebraic considerations to deduce, which renders
this argument very interesting. I'll try and concisely expose the main ones.
In the formula for $C(m,n,l)$ the limits on the summation index $i$ may algebraically be omitted, as they are intrinsic in the
two binomials when defined as
$$
\left( \begin{gathered}
x \\
q \\
\end{gathered} \right) = \left\{ {\begin{array}{*{20}c}
{x^{\,\underline {\,q\,} } /q!} & {\left| {\;0 \leqslant \text{integer}\,q} \right.} \\
\text{0} & {\left| {\;\text{otherwise}} \right.} \\
\end{array} } \right.
$$
which leaves more freedom in operating on the formula, while for computational purposes
we can fix them to $0 \leqslant i \leqslant m$. So we have better write:
$$
C(m,n,l)\quad \left| {\;0 \leqslant \text{integer}\;m,n,l} \right.\quad = \sum\limits_{\left( {0\, \leqslant } \right)\;i\,\,\left( { \leqslant \,m} \right)} {\left( { - 1} \right)^{\,i} \left( \begin{gathered}
m \\
i \\
\end{gathered} \right)\left( \begin{gathered}
\left( {m - i} \right)n \\
l \\
\end{gathered} \right)} \tag {1}
$$
Concerning the approaches in your post, note that the scheme leading to $C_1$ is over-shooting, because it makes distinction
between the ones of "first " and "second" introduction within each box, and that is difficult to compensate.
The Inclusion/Exclusion scheme is instead correct.
The example sketched indicates that the total number of arrangements can be partitioned into those that contain exactly $0$ empty boxes (${n}\choose {0}$ ways to choose that) and the associated $N(m,n,l)$ rows in the remaining boxes, plus
exactly $1$ empty boxes (${n}\choose {1}$ ways) and the associated $N(m-1,n,l)$ rows, ...,
$k$ empty boxes associated to $N(m-k,n,l)$ rows, for $k$ ranging from $0$ to $m$, so that we can write
$$
T(m,n,l) = \left( \begin{gathered}
n\,m \\
l \\
\end{gathered} \right) = \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,m} \right)} {\left( \begin{gathered}
m \\
k \\
\end{gathered} \right)C(m - k,n,l)} = \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,m} \right)} {\left( \begin{gathered}
m \\
k \\
\end{gathered} \right)C(k,n,l)} \tag {2}
$$
which is satisfied by (1).
This implicit relation can be inverted, using the binomial inversion theorem, giving
$$
\begin{gathered}
C(m,n,l) = \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,m} \right)} {\left( { - 1} \right)^{m - k} \left( \begin{gathered}
m \\
k \\
\end{gathered} \right)\left( \begin{gathered}
n\,k \\
l \\
\end{gathered} \right)} = \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,m} \right)} {\left( { - 1} \right)^k \left( \begin{gathered}
m \\
m - k \\
\end{gathered} \right)\left( \begin{gathered}
n\,\left( {m - k} \right) \\
l \\
\end{gathered} \right)} = \hfill \\
= \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,m} \right)} {\left( { - 1} \right)^k \left( \begin{gathered}
m \\
k \\
\end{gathered} \right)\left( \begin{gathered}
n\,\left( {m - k} \right) \\
l \\
\end{gathered} \right)} \hfill \\
\end{gathered} \tag {3}
$$
which provides a further confirmation of the validity of (1).
Referring to the scheme, we can infer an additional recurrence.
Consider to add an empty box aside the others, and move one ball at time from the original block to the new box.
Each configuration obtained is a partition of that corresponding to $m+1,n,l$, and the No. of rows is accounted by
$C(m,n,l-k) C(1,n,k)$.
The process goes on till the new box is full ($k=n$) or the original block is empty ($k=l$).
But we can waive these thresholds, as they are implicit in the product of the two $C$ factors, defined as in 1).
So we can write
$$
C(m + 1,n,l)\quad \left| {\;0 \leqslant \text{integer}\;m,n,l} \right.\quad =
\sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,l} \right)} {C(m,n,l - k)\;C(1,n,k)} \tag {4}
$$
which is a convolutory recurrence and which is satisfied by formula 1).
In fact, considering the layout of the boxes, it is clear that a more general recurrence holds:
$$
C(m + q,n,l)\quad \left| {\;0 \leqslant \text{integer}\;m,n,l,q} \right.\quad = \sum\limits_{\left( {0\, \leqslant } \right)\;k\,\,\left( { \leqslant \,l} \right)} {C(m,n,l - k)\;C(q,n,k)}
$$
To solve this recurrence autonomously, without recurring to the conjectured formula 1),
it remains to fix the initial conditions.
In the case of a single box, by definition $C(1,n,l)$ clearly is:
$$
C(1,n,l)\quad = \quad \begin{array}{*{20}c}
{n\backslash l} &| & 0 & {1 \leqslant l} \\
\hline
0 &| & 0 & 0 \\
{1 \leqslant n} &| & 0 & {\left( \begin{gathered}
n \\
l \\
\end{gathered} \right)} \\
\end{array} \quad \quad = \quad \left( \begin{gathered}
n \\
l \\
\end{gathered} \right) - \left( \begin{gathered}
0 \\
l \\
\end{gathered} \right)
$$
then it is easy to check that the recurrence 4) gives as solution formula 1).
Note that in the case of having no box, i.e. $m=0$, formula 1) returns
$$
C(0,n,l)\quad = \quad \begin{array}{*{20}c}
{n\backslash l} &| & 0 & {1 \leqslant l} \\
\hline
0 &| & 1 & 0 \\
{1 \leqslant n} &| & 1 & 0 \\
\end{array} \quad \quad = \quad \left( \begin{gathered}
0 \\
l \\
\end{gathered} \right)
$$
i.e. that the "empty" box is filled with $0$ balls (which is a usual concept in combinatorics) .
So $C(m,n,l)$ counts the arrangements with no empty box, and in case of keeping the definition
of with at least 1 ball per box then $m$ should be limited to be greater than $0$, or amended accordingly.