I might be missing the point of the question, or fail to see why what my computer does is not what the OP is looking for. Further this is is certainly not the most elegant solution, since I'm at work so I only had Windows & TeXnicCenter+MikTEX2.9 at my disposal. But I think it does what it should.
Here's what I do:
- Compile lua_pream.tex with profile
LuaTeX⇨PDF(pre) (see below)
- Compile lua_nopream.tex with profile
LuaTeX_post⇨PDF(post)
The profiles:
LuaTeX⇨PDF(pre) is
luatex -interaction=nonstopmode -ini -jobname="lua_pream" "&lualatex" mylatexformat.ltx "./lua_pream.tex"
or in TeXnicCenter:

LuaTeX_post⇨PDF(post) is
lualatex -fmt lua_pream "./lua_nopream.tex"
or in TeXnicCenter:

lua_nopream.tex contans not much really
\endofdump %%stuff from lua_pream.tex is dumped before here, you only need this if you have a local preamble
% part of the preamble that has to be evaluated each run
\begin{document}
The preamble used for this was compiled with vvvv set to \vvvv
\end{document}
lua_pream.tex contains the preamble
% static part of the preamble (stuff that does not change every now and then)
\documentclass{article}
\usepackage{luatexbase}
\usepackage{geometry}
\usepackage{amsmath,amsfonts,amsthm}
\usepackage{graphicx}
\usepackage{caption}
\usepackage{subfig}
\usepackage{booktabs}
\usepackage{enumitem}
\usepackage{xspace}
\usepackage{cleveref}
\usepackage{hyperref}
\usepackage{natbib}
\def\vvvv{foobar}
% the \endofdump part 'saves' everything above into one precompiled preamble, which gets loaded every time the LaTeX document is processed. This saves a lot of time mostly.
% NOTE: the following line ends the dumping into the preamble format file!
\endofdump
\begin{document}
This text plays no role I guess
\end{document}
mylatexformat. – Martin Schröder May 17 '13 at 09:08mylatexformatwith\usepackage{libertine}before\endofdump(TL 2013/pretest) – egreg May 17 '13 at 09:15microtype-package? In our case, this caused the largest performance drop (with LuaLaTeX). – Andy Dec 23 '13 at 19:28microtypesurely helped! – Ingo Jul 24 '14 at 08:58microtypeup so that it is pretty quick (or disabled, can't remember) ifdraftis active and will automatically activate withfinal. However, this can cause changes to page breaks, so some care is required. – cfr Sep 07 '15 at 15:16