do *not* enforce scalable fonts for T1 encoding, instead rely on cm-super fonts, which also provide underscore for non-tt font;
\documentclass[12pt,a4paper,fleqn]{report}
\usepackage[T1]{fontenc}
\usepackage{amssymb}
\usepackage{eurosym}
\usepackage[english]{babel}
\usepackage[only,bigsqcap]{stmaryrd}
\usepackage{textcomp}
\usepackage{latexsym}
\usepackage{graphicx}
\let\intorig=\int %iman.sty redefines \int
\usepackage{iman,extra,isar,proof}
\usepackage[nohyphen,strings]{underscore}
\usepackage{isabelle}
\usepackage{isabellesym}
\usepackage{railsetup}
\usepackage{ttbox}
\usepackage{supertabular}
\usepackage{style}
\usepackage{pdfsetup}
\hyphenation{Isabelle}
\hyphenation{Isar}
\isadroptag{theory}
\title{\includegraphics[scale=0.5]{isabelle_isar} \\[4ex] The Isabelle/Isar Reference Manual}
\author{\emph{Makarius Wenzel} \\[3ex]
With Contributions by
Clemens Ballarin,
Stefan Berghofer, \\
Jasmin Blanchette,
Timothy Bourke,
Lukas Bulwahn, \\
Amine Chaieb,
Lucas Dixon,
Florian Haftmann, \\
Brian Huffman,
Gerwin Klein,
Alexander Krauss, \\
Ond\v{r}ej Kun\v{c}ar,
Tobias Nipkow,
Lars Noschinski, \\
David von Oheimb,
Larry Paulson,
Sebastian Skalberg, \\
Christian Sternagel
}
\makeindex
\chardef\charbackquote=`\`
\newcommand{\backquote}{\mbox{\tt\charbackquote}}
\begin{document}
\maketitle
\pagenumbering{roman}
{\def\isamarkupchapter#1{\chapter*{#1}}\input{Preface.tex}}
\tableofcontents
\clearfirst
\part{Basic Concepts}
\input{Synopsis.tex}
\input{Framework.tex}
\input{First_Order_Logic.tex}
\part{General Language Elements}
\input{Outer_Syntax.tex}
\input{Document_Preparation.tex}
\input{Spec.tex}
\input{Proof.tex}
\input{Inner_Syntax.tex}
\input{Misc.tex}
\input{Generic.tex}
\part{Isabelle/HOL}\label{part:hol}
\input{HOL_Specific.tex}
\part{Appendix}
\appendix
\input{Quick_Reference.tex}
\let\int\intorig
\input{Symbols.tex}
\input{ML_Tactic.tex}
\begingroup
\tocentry{\bibname}
\bibliographystyle{abbrv} \small\raggedright\frenchspacing
\bibliography{manual}
\endgroup
\tocentry{\indexname}
\printindex
\end{document}