Let $\Omega$ be an open bounded subset of $\mathbb{R}^n$ with $C^1$ boundary. Let $$ \begin{matrix} F: \mathbb{R}^n \times \mathbb{R}^N \times \mathbb{R}^{nN} \to \mathbb{R},& \\ (x,z,p) \mapsto F(x,z,p)& \end{matrix} $$ be a $C^2$ Lagrangian corresponding to the functional $$ \mathcal{F}(u) = \int_{\Omega} F(x,u(x),Du(x)) dx $$ on the class $C^2(\bar{\Omega}, \mathbb{R}^N)$. By applying integration by parts and the divergence theorem (see Giaquinta and Hildebrandt, Chapter 1.2.4), we can show that if $u$ is an extrema, then $$ F_{p^i_\alpha}(x,u(x),Du(x)) \nu_\alpha = 0 \quad\text{ for }i = 1, \ldots, N, $$ where $\nu$ is the outward unit normal of $\partial \Omega$. Here, for fixed $1 \leq i \leq N$, $F_{p^i_\alpha}$ is a vector in $\mathbb{R}^n$ indexed by $\alpha$, and so $F_{p^i_\alpha} \nu_\alpha$ is a sum of $n$ vectors scaled by the components of $\nu$.
For example, when $N = 1$ and $$ F(x,z,p) = \sqrt{1 + |p|^2}, $$ then $\mathcal{F}(u)$ is the area of the graph of $u$, and the stationary points are functions whose graphs are minimal surfaces. The single vector field $F_p(x,u,Du)$ is $$ \frac{Du}{\sqrt{1 + |Du|^2}}, $$ which is the unit surface normal of the graph. The natural boundary condition $F_p \nu = 0$ translates into the statement that $F_p$ and $\nu$ are orthogonal. However, on the graph of $u$ defined as $$ \Gamma(u) = \{ (x,u(x)) : x \in \bar{\Omega} \} \subseteq \mathbb{R}^n \times \mathbb{R}, $$ the unit surface normal is given by $$ n = \frac{1}{\sqrt{1 + |Du|^2}}\left( Du , -1 \right), $$ and the normal to the boundary cylinder $\partial \Omega \times \mathbb{R}$ is $\bar{\nu} = (\nu, 0)$. Hence the boundary condition implies $n$ and $\bar{\nu}$ are also orthogonal, which means $\Gamma(u)$ and $\partial \Omega \times \mathbb{R}$ intersect perpendicularly.
In general Lagrangian problems, how are we supposed to interpret the vector fields $F_p$, particularly with general candidate solutions $u$? In principle, I wouldn't expect these vector fields to have a geometric relationship with the graph of $u$, yet the natural boundary conditions provide a geometric condition to check whether a candidate function is an extrema. Here, I'm ignoring questions regarding existence of solutions and regularity. I would presume that whatever interpretation is given has an appropriate weak analogue.