I want to draw a conclusion from an equivalent description of a relation.
Let $R$ be a relation on a set $M$ with $R \subseteq M \times M$.
First I have 2 examples of what I mean:
$x \sim_R y \Longleftrightarrow 1 = 1$, which obviously means $R = M \times M$
Let $M = \mathbb{N}$ and $F(x) = 1$ for all even $x \in \mathbb{N}$ and $0$ else.
$x \sim_R y \Longleftrightarrow F(x) = F(y)$
In this case it's easy to see, that $\sim_R$ is an equivalence relation, hence we were able to show the equivalence of $\sim_R$ to an equality.
But actually I want to be more abstract. I want to examine cases of the following:
$R$ is still a relation on a set $M$ with $R \subseteq M \times M$. It holds that:
$x \sim_R y \Longleftrightarrow F(x) = F(y)$ where $F(x), F(y)$ are 'missing word'.
What can $F(x), F(y)$ be? Sure, they are propositions, but they can't be any proposition, since you have to be able to compare $F(x)$ and $F(y)$ in terms of equality. How do I describe this circumstance mathematically correct?
It seems you're wondering about two different though related things, and are coming close to confusing them:
The answer to 2. is, absolutely yes. Regarding 1., however, I'm not sure what you mean, and your example about '$F(x)$ and $F(y)$ are "missing word"' is a bit confusing. This $F$ is supposed to have string values, in the alphabet $\{a,b,c,...,z\}$? What's its domain (what are $x,y$)?