The italic text letters come from the
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
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,
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
newtxmath continues to use the
txfonts math glyphs with many metric adjustments and some wholesale modifications.