In this context, "the same" means "isomorphic as $R$-modules", not "equal as subsets of $R$". Of course, they cannot be equal as subsets of $R$ for the reason you point out.
On a related point, the term "direct sum" actually has two different meanings. For simplicity, I will explain them only for binary direct sums. The first meaning is an "internal direct sum": a module $M$ is the internal direct sum of two submodules $N_1,N_2\subseteq M$ iff $N_1\cap N_2=0$ and $N_1+N_2=M$. The second meaning is an "external direct sum": if $N_1$ and $N_2$ are two modules, their external direct sum is the module $N_1\oplus N_2$ (or more generally, any isomorphic module) whose underlying set is cartesian product $N_1\times N_2$ and whose module structure is defined separately on each coordinate. The connection between the two definitions is that whenever $N_1$ and $N_2$ are submodules of $M$, there is a canonical homomorphism from the external direct sum $N_1\oplus N_2$ to $M$, and this homomorphism is an isomorphism iff $M$ is the internal direct sum of $N_1$ and $N_2$. And conversely, the external direct sum $N_1\oplus N_2$ is the internal direct sum of its two submodules $N_1'=N_1\times \{0\}$ and $N_2'=\{0\}\times N_2$ which are isomorphic to $N_1$ and $N_2$.
In an internal direct sum, obviously $N_1$ and $N_2$ must be distinct unless they are both $0$ (since $N_1\cap N_2=0$). However, when defining the external direct sum, it is perfectly fine if $N_1$ and $N_2$ are equal, as discussed in the other answers.