If the question is:
"For an arbitrary labeling of the nodes, so long as the root is the first, is the resulting matrix triangular?" The answer is no.
For instance, a simple counterexample is a graph with edges $\{(v_1, v_3), (v_3, v_2)\}$.
Then the adjacency matrix (as defined in the question) is
$\left[\begin{smallmatrix}
0 & 0 & 0\\
0 & 0 & 1\\
1 & 0 & 0\end{smallmatrix}\right]$.
In comments, you suggest the additional requirement that nodes are labeled so that destinations of an edge always come later than the source of the edge. In this case, the answer is yes, since every non-zero element of the matrix corresponds to an edge, and so the column index (the source node's label) is smaller than the row index (the destination node's label).
Moreover, such a labeling can be found for any directed (rooted) tree. You can stratify the tree into "layers", with the root in layer 0, all its neighbors in layer 1, all their children in layer 2, etc., and then number them (proceeding across each layer in succession.)
Another approach is to complete the partial order given by the tree to a linear order.