The covariance with respect to arbitrary coordinate transformations is expressed directly as the invariance of the potential one form $A = A_μ dx^μ$ and the field strength two-form $F = ½ F_{μν} dx^μ ∧ dx^ν$. They are geometric invariants just as much as is $dx^μ ∂_μ$. Correspondingly, the equations $dA = F$ and $dF = 0$ remain unchanged under arbitrary coordinate transforms. In any given coordinate system, their component forms are the equations you cited - with partial derivatives, not covariant derivatives.
There's no involvement of the metric at all. The operator "d" is an instance of a "natural operator" and the objects are called "natural objects". They are defined in a geometry at a much deeper level in which there is no notion of metrics, connections, parallelism, congruence, orthogonality, angle, speed or anything of the like.
Similarly, the response fields and sources arise at this level, too - out of the action principle, which is stated in integral form
$$S = \int L, \hspace 1em L = 𝔏 d^4x,$$
in terms of a Lagrangian 4-form $L$, with the Lagrangian density $𝔏$ being its component. They arise as the derivatives of the Lagrangian, and can be expressed in terms of the variational of the Lagrangian 4-form as:
$$ΔS = \int ΔL, \hspace 1em ΔL = (ΔA) ∧ J - (ΔF) ∧ G.$$
In 4-D, $J$ will be a 3-form ... the 3-current density, and $G$ will be a 2-form. You can read the second set of equations directly off of this as the Euler-Lagrange equations by integrating by parts:
$$(ΔF) ∧ G = (Δ(dA)) ∧ G = d(ΔA) ∧ G = d(ΔA ∧ G) + ΔA ∧ dG,$$
remembering that for odd-degree forms, such as $ΔA$, the Leibnitz rule has opposite sign:
$$d(ΔA ∧ \_) = d(ΔA) ∧ (\_) - ΔA ∧ d(\_).$$
Substituting back into the integral, this leads to:
$$ΔS = -\int d((ΔA) ∧ G) + \int (ΔA) ∧ (J - dG).$$
The boundary integral $\int d((ΔA) ∧ G)$ drops out from the analysis, leaving you with the Euler-Lagrange equation $J = dG$ and - as a consequence - $dJ = 0$.
All this is entirely non-metrical and lives at the deeper layer in geometry, so it involves no metrics or connections. In component form, the response field 2-form and source 3-form would be:
$$G = ½ 𝔊^{μν} ∂_ν ˩ ∂_μ ˩ d^4 x, \hspace 1em J = 𝔍^μ ∂_μ ˩ d^4 x,$$
where the contraction operator $(\_)˩(\_)$ is defined recursively by
$$∂_μ ˩ \left(dx^ν ∧ α\right) = δ_μ^ν α - dx^ν \left(∂_μ ˩ α\right), \hspace 1em ∂_μ ˩ f = 0,
$$
for differential forms $α$ and 0-forms/scalars $f$.
That's also a "natural operation" and is totally non-metrical. That's in contrast with the Hodge duality operator, which is given by
$$\star{\left(dx^μ ∧ ⋯ ∧ dx^ν\right)} = ∂^ν ˩ ⋯ ˩ ∂^μ \sqrt{|g|} d^4 x = g^{μμ'} ⋯ g^{νν'} ∂_{ν'} ˩ ⋯ ˩ ∂_{μ'} \sqrt{|g|} d^4 x,$$
where the dependence on a metric $g_{μν}$ is put clearly on display.
The forms $A$, $F$, $G$, $J$ are written in more familiar terms, as:
$$
A = 𝐀·d𝐫 - φ dt, \hspace 1em F = 𝐁·d𝐒 + 𝐄·d𝐫∧dt, \\
G = 𝐃·d𝐒 - 𝐇·d𝐫∧dt, \hspace 1em J = ρdV - 𝐉·d𝐒∧dt,
$$
where
$$d𝐫 = (dx, dy, dz), \hspace 1em d𝐒 = (dy∧dz, dz∧dx, dx∧dy), \hspace 1em dV = dx∧dy∧dz.$$
This corresponds to the coordinates, operators and components:
$$
t = x^0, \hspace 1em 𝐫 = (x, y, z) = \left(x^1, x^2, x^3\right), \\
\frac{∂}{∂t} = ∂_0, \hspace 1em ∇ = \left(\frac{∂}{∂x}, \frac{∂}{∂y}, \frac{∂}{∂z}\right) = \left(∂_1, ∂_2, ∂_3\right), \\
φ = -A_0, 𝐀 = \left(A_x, A_y, A_z\right) = \left(A_1, A_2, A_3\right), \\
𝐁 = \left(B^x, B^y, B^z\right) = \left(F_{23}, F_{31}, F_{12}\right),
𝐄 = \left(E_x, E_y, E_z\right) = \left(F_{10}, F_{20}, F_{30}\right), \\
𝐃 = \left(D^x, D^y, D^z\right) = \left(𝔊^{01}, 𝔊^{02}, 𝔊^{03}\right),
𝐇 = \left(H_x, H_y, H_z\right) = \left(𝔊^{23}, 𝔊^{31}, 𝔊^{12}\right), \\
ρ = 𝔍^0, \hspace 1em 𝐉 = \left(J^x, J^y, J^z\right) = \left(𝔍^1, 𝔍^2, 𝔍^3\right),
$$
except that $x$, $y$, $z$ don't have to be Cartesian coordinates - or even space-like coordinates at all, nor does $t$ have to be a time-coordinate or even time-like. They can denote any four independent functions of the coordinates.
You ask: how, then, does one get light-speed motion out of this, if there is no metric-dependence or any reference to such primitives of chrono-geometry, such as orthogonality, space-like versus time-like, speed, congruence, distance, etc.? The answer is that it doesn't come from there.
The empirical content conveyed by the theory doesn't reside with those equations at all! They're just a framework. The only actual empirical statement being made by them is that the system in question (here: the electromagnetic field) actually has those attributes $A$ (and, thus $F$) as part of its description, and that its dynamics is described in terms of some first-order Lagrangian (and thus, that there should be $G$ and $J$ involved in the description of its dynamics).
The content resides with the Lagrangian, and with the relations conveyed by them; namely, the constitutive relations, here expressed in general form in terms of the Lagrangian density by:
$$ρ = -\frac{∂𝔏}{∂φ}, \hspace 1em 𝐉 = \frac{∂𝔏}{∂𝐀}, \hspace 1em 𝐃 = \frac{∂𝔏}{∂𝐄}, \hspace 1em 𝐇 = -\frac{∂𝔏}{∂𝐁}.$$
In contrast to the equations already laid out, they are not symmetric under arbitrary coordinate transforms. In fact, the whole point behind the choice of $𝔏$ is to call out a specific set of symmetries: gauge symmetry and Lorentz symmetry.
Gauge symmetry - i.e. symmetry under gauge transforms:
$$δA = -dχ \hspace 1em⇒\hspace 1em (δφ, δ𝐀) = \left(\frac{∂χ}{∂t}, -∇χ\right),$$
mandates that an $𝔏$ that is a function of $A$ and its first derivatives (and other fields that have non-trivial tranforms under this gauge transform) may not depend directly on $A$, may depend on the gradients of $A$ only in the anti-symmetric combinations $∂_μ A_ν - ∂_ν A_μ$ that make up the components of $F$, and may depend on the gradients $∂q$ of other fields $q$ that have non-trivial transforms under $χ$ only through their gauge-covariant derivatives $∇_A q = ∂q + (⋯A⋯q⋯)$ (out of which, an indirect dependency on $A$ in the Lagrangian may arise).
That's an instance of Utiyama's Theorem.
The requirement of Lorentz symmetry mandates that the Lagrangian's dependence on $F$ only be through its Lorentz invariants:
$$ℑ^1 = \frac{E^2 - B^2 c^2}{2}, \hspace 1em ℑ^2 = 𝐁·𝐄,$$
and that most definitely breaks general coordinate covariance and calls out a specific geometry and has explicit dependence on a metric - one that is locally Minkowski.
For instance, a Lagrangian density that has the general form:
$$𝔏 = 𝔏_0\left(ℑ^1, ℑ^2\right) + 𝔏_1\left(q, ∇_Aq\right),$$
that yield constitutive relations of the form:
$$ρ = -\frac{∂𝔏_1}{∂φ}, \hspace 1em 𝐉 = \frac{∂𝔏_1}{∂𝐀}$$
for the sources, which depends on what extra fields are present, and will have response fields determined by the derivatives of $𝔏_0$:
$$ε_1 = \frac{∂𝔏_0}{∂ℑ^1}, \hspace 1em ε_2 = \frac{∂𝔏_0}{∂ℑ^2},$$
given by:
$$𝐃 = ε_1 𝐄 + ε_2 𝐁, \hspace 1em 𝐇 = ε_1 c^2 𝐁 - ε_2 𝐄,$$
where $ε_1\left(ℑ^1, ℑ^2\right)$ and $ε_2\left(ℑ^1, ℑ^2\right)$ are generally functions of the invariants $ℑ^1$ and $ℑ^2$ satisfying:
$$\frac{∂ε_1}{∂ℑ^2} = \frac{∂ε_2}{∂ℑ^1}.$$
You'll recognize $ε_1$ as the permittivity, while $ε_2$ is the axial (parity-violating) version of permittivity.
For null fields $ℑ^1 = 0$ and $ℑ^2 = 0$, these reduce to constants, $ε_1(0, 0)$ and $ε_2(0, 0)$, the latter which can be set to 0, by just redefining the response fields as:
$$𝐃 → 𝐃 - ε_2(0, 0) 𝐁, \hspace 1em 𝐇 → 𝐇 + ε_2(0, 0) 𝐄,$$
without affecting the Euler-Lagrange equations.
That essentially recovers the constitutive relations:
$$𝐃 = ε_0 𝐄, \hspace 1em 𝐁 = μ_0 𝐇, \hspace 1em ε_0 = ε_1(0, 0), \hspace 1em μ_0 = \frac{1}{ε_1(0,0)c^2},$$
that comes out of the Maxwell-Lorentz Lagrangian density:
$$\frac{ε_0|𝐄|^2}{2} - \frac{|𝐁|^2}{2μ_0}.$$
That's where the metric-dependence resides ... and where all the metric-dependence is confined to. That's where the light speed trajectories arise from.
It's coming out of the constitutive laws, not out of the other equations.