If i understand correctly the Levi-Civita symbol is the function $\varepsilon : \{0, \dots, 3\}^4 \to \{-1,0,1\}$ that that sends a permutation of $\{0,\dots,3\}$ to its sign and non-permutations to 0.
Since it is a function and not a tensor (and not even defined on the manifold) its "upper" or "lower" indices have no actual meaning and are only a tool used for convenience to use the summation convention. We define the Levi-Civita symbol with any combination of upper and lower indices to be the same function that sends the indices to $\varepsilon( \mathrm{indices})$.
Now $g_{mn}$ is not the metric tensor, rather it is a component function of the metric tensor that is to say it is a smooth function $g_{mn} : M \to \mathbb{R}$, where $M$ is our manifold. So that locally $g = g_{mn} dx^m \otimes dx^n$ where $x^0, \dots , x^3$ is some coordinate system and $g$ is the metric tensor.
Now the expression $g_{mn} \varepsilon^{npqr}$ is totally degenerate because it depends on the choosen basis. It is simply a function (that for fixed $m, p,q,r$) sends a point $s$ on $M$ to the number $g_{mn}(s) \varepsilon^{npqr}$.
The index lowering/increasing isomorphism acts on (non degenerate) tensor fields and not on functions and especially not on functions that are not defined on the manifold.