I think you've got a few things slightly mixed up, which made your question a bit unclear.
I don't like the heuristic that the flat norm 'computes minimal surfaces'. For one, it's not true that the flat norm of a boundary is always realized by a minimal surface. That is, in general you only have the inequality
\begin{equation}
F(A)
\leq \inf \, \{ \mathbf{M}(T) \mid \partial T = A \}.
\end{equation}
For example, take a circle $C_R \subset \mathbf{R}^2$ of radius $R > 0$ in the Euclidean plane. Let $A = C_R$ be this circle. This spans only one minimal surface, namely the disk $D_R$. However, if you compare their masses, you find that $\mathbf{M}(C_R) = \mathcal{H}^1(C_R) = 2 \pi R$, while $\mathbf{M}(D_R) = \mathcal{H}^2(D_R) = \pi R^2$.
You will find the same behavior if you rescale an arbitrary boundary $A = \partial Q$. This is because there is a second inequality, which 'competes' with the one above:
\begin{equation}
F(\partial Q) \leq \mathbf{M}(\partial Q).
\end{equation}
If you rescale $\partial Q$ by $\lambda > 1$, then the right-hand side changes like
\begin{equation}
\mathbf{M}(\lambda \cdot \partial Q)
= \lambda^k \mathbf{M}(\partial Q),
\end{equation}
whereas the bound from the inequality grows quicker:
\begin{equation}
\inf \, \{ \mathbf{M}(T) \mid \partial T = \lambda \cdot \partial Q \}
= \lambda^{k+1} \inf \, \{ \mathbf{M}(T) \mid \partial T = \partial Q \}.
\end{equation}
Therefore, if you take $\lambda$ large enough, you will get the strict inequality
\begin{equation}
F(\lambda \cdot \partial Q)
< \inf \, \{ \mathbf{M}(T) \mid \partial T = \lambda \cdot \partial Q \}.
\end{equation}
(In general it's a good idea with these things to check how they behave under homothetic rescalings.)
To get a better feel for the flat norm, here are some questions that should be helpful to think about.
What is the flat norm of two disks in $\mathbf{R}^3$, lying above one another? How does it depend on the radius, and the distance between them? Does it depend on their orientations? What if they are given multiplicities?
In general, I would suggest spending some time thinking about the flat distance. For example, say the disks above lie a distance $1/j$ apart. What is their limit (with respect to the flat distance) as $j \to \infty$? Does it depend on their orientations, or possible multiplicities?
Another potentially useful example you get by considering the graph of a function $u: D_1 \to \mathbf{R}$, denoted $G$. Assuming $G$ is close to $D_1 \times \{ 0 \}$ in the flat distance, what information is gained on $u$? Does it give you a bound almost everywhere, in $L^p$, etc.? Does it give you a bound for the area of $G$? If you have a sequence $(u_j)$, and $G_j \to D_1 \times \{ 0 \}$ as $j \to \infty$, does this mean $u_j \to 0$? And in what topology?
As far as references are concerned, I am assuming you are aware of Leon Simon's lecture notes on GMT. You could also take a look at Frank Morgan's book; also I believe Otis Chodosh has some lecture notes from a course taught by Brian White that you might enjoy.