This is my LaTeX template for responding to reviewers. I have extended several macros that I found on stackexchange to allow LaTeX style cross referencing between reviewers points. Here is an example zip file that can be directly imported into Overleaf and here is how it looks:

Note the circle in red which is the reference inserted with the \ref tag.

The source code

Download: rebuttal.zip

% LaTeX rebuttal letter example. 
% 
% Copyright 2019 Friedemann Zenke, zenkelab.org
%
% Based on examples by Dirk Eddelbuettel, Fran and others from 
% https://tex.stackexchange.com/questions/2317/latex-style-or-macro-for-detailed-response-to-referee-report
% 
% Licensed under cc by-sa 3.0 with attribution required.

\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage{lipsum} % to generate some filler text
\usepackage{fullpage}

% import Eq and Section references from the main manuscript where needed
% \usepackage{xr}
% \externaldocument{manuscript}

% package needed for optional arguments
\usepackage{xifthen}
% define counters for reviewers and their points
\newcounter{reviewer}
\setcounter{reviewer}{0}
\newcounter{point}[reviewer]
\setcounter{point}{0}

% This refines the format of how the reviewer/point reference will appear.
\renewcommand{\thepoint}{P\,\thereviewer.\arabic{point}} 

% command declarations for reviewer points and our responses
\newcommand{\reviewersection}{\stepcounter{reviewer} \bigskip \hrule
                  \section*{Reviewer \thereviewer}}

\newenvironment{point}
   {\refstepcounter{point} \bigskip \noindent {\textbf{Reviewer~Point~\thepoint} } ---\ }
   {\par }

\newcommand{\shortpoint}[1]{\refstepcounter{point}  \bigskip \noindent 
	{\textbf{Reviewer~Point~\thepoint} } ---~#1\par }

\newenvironment{reply}
   {\medskip \noindent \begin{sf}\textbf{Reply}:\  }
   {\medskip \end{sf}}

\newcommand{\shortreply}[2][]{\medskip \noindent \begin{sf}\textbf{Reply}:\  #2
	\ifthenelse{\equal{#1}{}}{}{ \hfill \footnotesize (#1)}%
	\medskip \end{sf}}

\begin{document}

\section*{Response to the reviewers}
% General intro text goes here
We thank the reviewers for their critical assessment of our work. 
In the following we address their concerns point by point. 

% Let's start point-by-point with Reviewer 1
\reviewersection

% Point one description 
\begin{point}
	\lipsum[1]
	\label{pt:foo}
\end{point}

% Our reply
\begin{reply}
	We agree with the reviewer on this important point. This is what we did to
	fix it. 
	\lipsum[2]
\end{reply}

\begin{point}
	Reviewer \thereviewer's second point.
	\label{pt:bar}
\end{point}

\begin{reply}
	And our reply to it.
\end{reply}

\subsection*{Minor}

% Use the short-hand macros for one-liners.
\shortpoint{ Typo in line xy. }
\shortreply{ Fixed.}

% Begin a new reviewer section
\reviewersection

\begin{point}
	This is the first point of Reviewer \thereviewer. With some more words foo
	bar foo bar ...
\end{point}

\begin{reply}
	Our reply to it with reference to one of our points above using the \LaTeX's 
	label/ref system (see also \ref{pt:foo}).
\end{reply}

\end{document}