For any $\mathbb Z_2$-valued function $f$ on the set of segments $[v,v+e_i]$ for $v\in \mathbb Z^3$ and $i=1,2,3$, and any $S$ that bounds $C$
$$
\sum_{P\in S}\sum_{edge\in P} f(edge)
$$
is independent of the choice of $S$ (it is equal to the sum of $f$ over the segments of $C$).
Thus to prove the independence of parity of the area from the choice of $S$, it suffices to find a function on the set of (directed) segments $[v,v+e_i]$ such that the sum of it over edges of any size one lattice square is $1\in \mathbb Z_2$.
One way of thinking about such $f$ is the following homological algebra construction. If you naively tensor three complexes, then the corresponding squares will commute rather than anticommute. However, it is possible to change some of the signs to make the total complex to be an actual complex. The edges that needed to be altered are the ones that will have $f=1$.
For a more elementary argument, we will declare $f([v,w])$ to be $1$ if and only if $[v,w]$ is equal modulo $2$ to one of the following:
$$
[(0,0,0),(1,0,0)],~[(0,0,1),(0,1,1)],~[(0,1,1),(1,1,1)],
$$
$$
[(1,0,0),(0,0,0)],~[(0,1,1),(0,0,1)],~[(1,1,1),(0,1,1)],
$$
I will now argue that every lattice square contains exactly one such edge.
Note that the set above is preserved by translations by elements of $2\mathbb Z^3$.
It is also preserved by symmetries across lattice planes, as these have an effect of switching $[v,w]$ and $[w,v]$ modulo $2$ or preserving $[v,w]$ modulo $2$. Every lattice square can be moved into one of the six facets of the standard cube $[0,1]^3$ by the above shifts and symmetries. It remains to observe that each of the faces of the standard cube contains exactly one edge from the first line and none from the second line.