The italic text letters come from the OT1
(or T1
) font with it
shape, while the math letters
from the OML
encoded font (also with the it
shape). Although they look very similar, they are not necessarily identical: for example, overlapping the text-italic and the math-italic S
in Computer Modern shows that the math version is somewhat broader
\documentclass{article}
\usepackage{xcolor}
\begin{document}
\makebox[0pt][l]{\color{red}\textit{S}}$S$
\end{document}

Furthermore, even they were identical in shape their bounding boxes would in general differ (sometimes a lot), as the following snippet shows for Computer Modern, txfonts
and newtx
:
\documentclass{article}
\begin{document}
\setlength{\fboxsep}{-\fboxrule}
\mathsurround=0pt
CM: {\usefont{OT1}{cmr}{m}{it}\fbox{S}}
{\usefont{OML}{cmm}{m}{it}\fbox{S}}
tx: {\usefont{OT1}{txr}{m}{it}\fbox{S}}
{\usefont{OML}{txmi}{m}{it}\fbox{S}}
newtx: {\usefont{OT1}{ntxtlf}{m}{it}\fbox{S}}
{\usefont{OML}{ntxmi}{m}{it}\fbox{S}}
\end{document}

In the case of the tx
fonts, it is clear that the bounding box of the math-italic S
leaves a large empty space on the right of the glyph.
Coming to your question
However, I was wondering if this is to be considered as a flaw in one of the font metrics, or if this is the sort of thing a user is expected to "roll with"?
I would say that it is a (poor?) design choice of the font. I won't go as far as to call it a flaw ;-)
because maybe there was a rationale behind it. Anyway, when I type math in a Times setting (well, never, but if I had to) I use the newtx
fonts. The text version (newtxtext
) is nowadays based on the TeX Gyre Termes, but (quote from the newtx
documentation)
newtxmath
continues to use the txfonts
math glyphs with many metric adjustments and some wholesale modifications.
S
withtxfonts
is quite larger than the letter itself. Fixing such things is in part what led tonewtx
; so in a sense I'd say, as you wonder, that this is in fact a flaw in thetxfonts
.$S$
and not\textit{S}
, if it is the underlyingS
that is at fault?txfonts
.