Load microtype after fonts.

Microtype needs to know what fonts are in use and it is suggested that it is aded after loading fonts.

default.latex

@@ -4,8 +4,6 @@
 \usepackage{amssymb,amsmath}
 \usepackage{ifxetex,ifluatex}
 \usepackage{fixltx2e} % provides \textsubscript
-% use microtype if available
-\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
 % use upquote if available, for straight quotes in verbatim environments
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
 \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
@@ -33,6 +31,8 @@ $if(mathfont)$
     \setmathfont{$mathfont$}
 $endif$
 \fi
+% use microtype if available
+\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
 $if(geometry)$
 \usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
 $endif$