Yes, there are other cases.
Superposition and entanglement
The proposed rule
$$
\text{if $U$ has an element $U_{ij}$ such that $|U_{ij}|\notin\{0,1\}$},\\ \text{then the set $\{T,U\}$ is universal}\tag1
$$
appears motivated by the observation that any set of permutation gates with phases fails to create superposition states when acting on a computational basis state. However, the rule $(1)$ doesn't work, because the ability to create superpositions is necessary but not sufficient for universality. For example, any product unitary such as
$$
H\otimes H=\frac12\begin{bmatrix}
1&1&1&1\\
1&-1&1&-1\\
1&1&-1&-1\\
1&-1&-1&1
\end{bmatrix}\tag2
$$
fails to create entanglement so $\{T, H\otimes H\}$ fails to be universal.
Stuck in a subspace
In fact, the ability to create superpositions and entanglement is still not sufficient. A gateset may fail to be universal by failing to act transitively on quantum states. For example, if $V=\begin{bmatrix}a&b\\c&d\end{bmatrix}\in U(2)$, then $\{T,U\}$ with
$$
U=\begin{bmatrix}
1&&&\\
&a&b&\\
&c&d&\\
&&&1
\end{bmatrix}\tag3
$$
is not universal even though $U$ may create entangled states. This follows from the observation that all circuits consisting of $T$ and $U$ preserve$^1$ the number of $0$s and $1$s of an input state in the computational basis. In particular, any such circuit maps $|0\dots 0\rangle$ to itself.
$^1$ Gates of the form $(2)$ are sometimes called "excitation-preserving", because they map each state with $k=0,1,2$ qubits in the $1$ state to a state where $k$ qubits are in the $1$ state.