If I understand correctly, something like this where the annotated version picks up even non standard settings of the second example.

\documentclass{article}
\usepackage{amsmath}
\usepackage{xcolor}
\definecolor{color1}{RGB}{219, 48, 122}
\definecolor{color2}{RGB}{48, 122, 219}
\definecolor{color3}{RGB}{200,0,0}
\newcommand{\isnoun}[1]{\ensuremath{\overset{\makebox[0pt]{\scriptsize\color{color1}\textbf{N}}}{\strut\text{#1}}}}
\newcommand{\isverb}[1]{\ensuremath{\overset{\makebox[0pt]{\scriptsize\color{color2}\textbf{V}}}{\strut\text{#1}}}}
% new command comma, plus sign and period
\newcommand{\iscomma}[1]{\ensuremath{\overset{\makebox[0pt]{\scriptsize\color{color3}\textbf{P}}}{\strut\text{#1}}}\spacefactor\sfcode`#1 }
\let\isplusign\iscomma
\let\isperiod\iscomma
\begin{document}
Japan is a country, France is a country.
Japan is a country, France is a country.
Japan is a country, France is a country.
Japan is a country, France is a country.
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\bigskip
% big sentence space
\spaceskip=1em plus .5em minus .2em
\xspaceskip=2em plus 1em minus .1em
Japan is a country, France is a country.
Japan is a country, France is a country.
Japan is a country, France is a country.
Japan is a country, France is a country.
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\isnoun{Japan} \isverb{is} a country\iscomma{,} \isnoun{France} \isverb{is} a country\isperiod{.}
\end{document}