It's possible to give "formal" proofs of this result that don't actually deal with the issue you're talking about. So it helps to pay attention to the details of that argument, and to handle them in the "right" way.
[I will assume we are dealing with von Neumann algebras on separable Hilbert spaces only--- mainly because I haven't ever really thought about the more general case.]
Let $M$ be a factor with a minimal projection on a Hilbert space $H$. Let $\{p_i: i \in I\}$ be a maximal family of mutually orthogonal minimal projections in $M$. By hypothesis the set $I$ is either finite or countable. So I will assume $I$ is either the set of positive integers, or the set $\{1,2,\dots,n\}$ for some finite $n$.
Arguments you are probably familiar with show that all of the projections $p_i$, $i \in I$, are Murray-von Neumann equivalent to one another, and the partial isometries implementing these equivalences give rise to a system of matrix units in $M$, allowing you to "think of elements of $M$ as block matrices" and thus get a map from $M$ to $\mathcal{B}(\ell^2(I))$...
But it's simpler from a technical point of view to complete the following program:
Prove that the partial isometries implementing the equivalences among the $p_i$, $i \in I$, generate $M$ as a von Neumann algebra.
Observe (or prove) that the space $H$ decomposes as an orthogonal direct sum $ H = \bigoplus_{i \in I} p_i H, $ so there is unitary $U$ from the Hilbert space $K = \ell^2(I) \otimes p_1 H$ (the Hilbert space tensor product) to $H$ satisfying $ U (c_i \otimes \eta) = e_{i1} \eta, \qquad i \in I, \quad \eta \in p_1 H, $ where here for each $i \in I$, I let $c_i$ denote the element of $\ell^2(I)$ that is $1$ at $i$ and $0$ elsewhere (this is sort of the "usual" orthonormal basis of $\ell^2(I)$) and $e_{i1}$ denotes the matrix unit in $M$ with initial space $p_1 H$ and final space $p_i H$.
It immediately follows from 1. and 2. that $U^* M U$ ($ = \{U^* m U: m \in M\}$) is a von Neumann subalgebra of $\mathcal{B}(K)$ generated by the operators $U^* e_{ij} U$, $i, j \in I$.
Do a calculation that shows for each $i, j \in I$ that $U^* e_{ij} U$ is just the operator $E_{ij} \otimes \operatorname{id}$ on $\mathcal{B}(K)$, where $\{E_{ij}: i, j \in I\}$ is the usual system of matrix units in $\mathcal{B}(\ell^2(I))$ coming from the orthonormal basis $\{c_i: i \in I\}$ and $\operatorname{id}$ denotes the identity operator on $p_1 H$.
You know (as a special case of 1.) that the operators $E_{ij} \otimes \operatorname{id}$, $i, j \in I$, generate the von Neumann subalgebra $\mathcal{B}(\ell^2(I)) \otimes \operatorname{id}$ of $\mathcal{B}(K)$.
So not only is $M$ "isomorphic to" some $\mathcal{B}(\ell^2(I))$, but we can write down a specific unitary operator between the Hilbert space on which $M$ acts and the Hilbert space $\ell^2(I) \otimes p_1 H$ that implements the isomorphism.
Note that the unitary implementing the isomorphism is not, generally, coming from a unitary between $H$ and $\ell^2(I)$. This makes intuitive sense, though: for example, the von Neumann subalgebra of $\mathcal{B}(H)$ (with $H$ infinite dimensional) generated by two mutually orthogonal equivalent projections summing to $1$ is clearly isomorphic (as an complex algebra) to $\mathcal{B}(\mathbb{C}^2)$, but there is no hope of finding a unitary from $H$ to $\mathbb{C}^2$. This isomorphism exists only in the world of abstract algebra: it is not spatial. And in some contexts, you only want to consider spatial isomorphisms (ones implemented by unitaries in the above way) as your "isomorphisms."
You are right to find it sort of "fishy" when people write down maps between von Neumann algebras that using "matrix theoretic" formulas on generators and don't comment on issues like these. But, when algebraic formulas work, very often it is because there is a unitary between some underlying Hilbert spaces that implements the formulas (and, to find the all-details-included proof, you often just need to identify or construct the relevant Hilbert spaces). It is trivially true that maps of the form $x \mapsto U^* x U$, with $U$ unitary, map von Neumann algebras to von Neumann algebras, and play nice with all the topologies. If you do it right, that is what is going on here.
I hope this helped.