What you call Beth’s theorem in the first paragraph is in fact trivial: just take for $\psi$ the sentence $\phi$ where all instances of $R$ are replaced by $\bot$ (or any fixed $\Sigma$-formula, for that matter).
The proper way to formulate Beth’s theorem along these lines is as follows:
(B1) Let $\Sigma\subseteq\Sigma^*$ be two languages, $T$ a theory in $\Sigma^*$, and $\phi$ a $\Sigma^*$-sentence. Assume that for every pair of models $M,N\models T$ such that $M\let\res\restriction\res\Sigma\simeq N\res\Sigma$, $M\models\phi$ iff $N\models\phi$. Then there exists a $\Sigma$-sentence $\psi$ such that $M\models\phi\let\eq\leftrightarrow\eq\psi$ for every model $M\models T$.
This is also more or less the version given on Wikipedia, except they use $=$ instead of $\simeq$, and allow formulas with free variables (both of which are immaterial differences). The presence of $T$ (and specifically the fact that it may not be a $\Sigma$-theory) is essential, otherwise the result is trivial, as mentioned above.
The second form of Beth’s theorem, in the “at most one” version, can be stated as follows:
(B2) Let $\Sigma\subseteq\Sigma^*$ be two languages, $T$ a theory in $\Sigma^*$, and $R\in\Sigma^*$. Assume that $R^M=R^N$ for every pair of models $M,N\models T$ such that $M\res\Sigma=N\res\Sigma$. Then there exists a $\Sigma$-formula $\psi$ such that $R^M=\psi^M$ for every model $M\models T$.
Note that in both (B1) and (B2), a simple application of compacteness shows that we could assume without loss of generality that $T$ is finite, hence in (B2), $T$ plays the role of your $\phi$. The only remaining difference is that I allow $\Sigma^*$ to be larger than $\Sigma\cup\{R\}$.
Now it is easy to see that (B1) and (B2) are equivalent.
(B1)${}\Rightarrow{}$(B2): If $\Sigma,\Sigma^*,T,R$ satisfy the assumptions of (B2), choose new constants $\vec c$ corresponding to the variables of $R$, and put $\Sigma'=\Sigma\cup\{\vec c\}$, $\Sigma'^*=\Sigma^*\cup\{\vec c\}$, $\phi=R(\vec c)$. Then the assumptions of (R1) are satisfied for $\Sigma',\Sigma'^*,T,\phi$, hence there exists a $\Sigma'$-sentence $\psi(\vec c)$ equivalent to $\phi$ in models of $T$ (expanded to $\Sigma'$), which means $R(\vec x)$ is equivalent to $\psi(\vec x)$ in models of $T$ in the original language.
(B2)${}\Rightarrow{}$(B1): Given $\Sigma,\Sigma^*,T,\phi$ satisfying the assumptions of (B1), let $\Sigma'=\Sigma^*\cup\{R\}$, where $R$ is a new nullary predicate, and $T'=T\cup\{\phi\eq R\}$. Then (B2) implies that there is a $\Sigma$-formula $\psi$ (which may be assumed to have the same free variables as $R$, i.e., none) equivalent to $R$ in models of $T'$. Since every model of $T$ can be expanded to a model of $T'$, this implies that $\psi$ is equivalent to $\phi$ in models of $T$. (If you do not like nullary predicates, you can make do with unary just the same.)
The two versions of Beth’s theorem can also be restated syntactically. Let $\Sigma^*\smallsetminus\Sigma=\{R_i:i\in I\}$, and let $R'_i$ be new predicates with matching arity. In order not to burden the notation too much, I will write formulas or theories in $\Sigma^*$ or $\Sigma\cup\{R'_i:i\in I\}$ in the form $\phi(\vec R)$, as if these predicates were second-order free variables. Then (B1) is equivalent to:
(B1’) If $T(\vec R),T(\vec R')\vdash\phi(\vec R)\eq\phi(\vec R')$, there is a $\Sigma$-sentence $\psi$ such that $T(\vec R)\vdash\phi(\vec R)\eq\psi$,
and (B2) is equivalent to
(B2’) If $T(\vec R),T(\vec R')\vdash R_i(\vec x)\eq R'_i(\vec x)$, there is a $\Sigma$-formula $\psi$ such that $T(\vec R)\vdash R_i(\vec x)\eq\psi(\vec x)$.