As I said in the comments, this is an answer I prepared to the original question.
Maybe you could consider having two separate main files, to be used with XeLaTeX or LuaLaTeX (e.g. your own copy that you could host and distribute), and pdflatex respectively:
xelatex main_xelatex.tex
pdflatex main_pdflatex.tex
The changes required to switch from one to the other are certainly not comparable to the hassle of having to switch between LaTeX and Word; it is rather quite small all in all. I have been doing that, personally.
You can then e.g. write your document's contents in a manuscript.tex file and use \input manuscript.tex in between begin{document} and end{document} to include the actual contents in both your setups.
You can moreover easily reuse this setup for your later publications.
I have just written a MWE demo for you. There are more elaborate ways to do it, but this is simple and works.
main_xelatex.tex
\documentclass[11pt, a4paper]{article}
\usepackage{fontspec}
\usepackage{microtype}
\usepackage{xltxtra}
\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{mathrsfs}
\usepackage{latexsym}
\usepackage{euscript}
\usepackage{lipsum}
\title{Lorem Ipsum}
\author{René Descartes}
\begin{document}
\setmainfont{TheSansOsF} % or any other font you want XeLaTeX to use.
\input manuscript.tex
\end{document}
Note that in this example main_xelatex.tex is compatible with both XeLaTeX and LuaLaTeX.
main_pdflatex.tex
\documentclass[11pt, a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{mathrsfs}
\usepackage{latexsym}
\usepackage{euscript}
\usepackage{lipsum}
\title{Lorem Ipsum}
\author{René Descartes}
\begin{document}
\input manuscript.tex
\end{document}
manuscript.tex
\maketitle
\begin{abstract}
\lipsum[1]
\end{abstract}
\section{Introduction}
\lipsum[2-4]
% ETC ...
XeLaTeX output

pdflatex output

I am essentially always using XeLaTeX nowadays when writing documents, knowing it's easy to switch if needed (since I only input text, pictures, and maths). Of course, if you know for sure that what you are currently writing is for a paper in a specific journal, then contacting them beforehand is the safest approach I would say.