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 how it looks:
Note the circle in red which is the reference inserted with the \ref tag.
The source code
% LaTeX rebuttal letter example.
% 2018 fzenke.net
\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}