Why aren't the topological boundary of a manifold with boundary and the boundary of the manifold the same sets?
We defined the boundary of a manifold as follows:
$\partial M:= \lbrace p \in M : \exists (U,\varphi) \text{chart with} \varphi (p)=(0,...,x_n)^T \rbrace$
In contrast to the topological boundary being the closure minus the interior of M.
Take a simple example that lives in both situations. If $X$ is any topological space, the topological boundary of $X$ is $\varnothing$. Now, consider the case $X=[0,1]$ endowed with the inherited Euclidean subspace topology. This is also the simplest example of a $1$-manifold with boundary. As I said earlier, the topological boundary is $\varnothing$. However, the manifold boundary is the $2$-point set $\{0,1\}$. If you instead regard $[0,1]$ as a subset of the space $\mathbb{R}$ then its topological boundary is $\{0,1\}$, which is where your confusion lies.