The standard definition depends on the font encoding: With OT1 and T1 it is an accent (you can find the definitions in OT1enc.def and T1enc.def). When you use a newer fontspec(which loads xuniode) and so EU1 (xelatex) or EU2 (lualatex) fontencoding the general definition of \. is that it is a "combining dot":
\DeclareEncodedCompositeCharacter{\UTFencname}{\.}{0307}{02D9} % Combining dot above
Some special combinations are mapped to specific glyph. E.g. \.e is Unicode U+0117:
\DeclareUTFcomposite[\UTFencname]{x0117}{\.}{e}
In theory is should be possible to rewrite the commands so that they check if the glyphs are available and use some fallback if not. In practice I doubt that it is sensible. It wouldn't help if you enter the glyphs directly instead of using accent commands, it would slow down compilation, it would mean a lot work to decide and implement sensible fallbacks in xunicode (and it would make xunicode much larger). If you want to use non-standard characters with xelatex the best is to use a font which has the glyphs. If a small number are missing add fallbacks based on the method suggested in the question you linked to.
Edit: Actually the question you linked to suggested to redefine \d with \renewcommand. This is not a good idea as it affects the definition of \d in other encodings too. One should always use one of the various encoding dependant declarations. In the example below you should compare the difference between using the \renewcommand and the \DeclareTextCommand line on the OT1-encoded part. To solve you actual problem you could try the \DeclareTextAccent line. If your font has the dot accent it should work.
\documentclass{article}
\usepackage{fontspec}
\setmainfont{Garamond}
%\DeclareTextCommand{\.}{\UTFencname}[1]{(#1)}
%\renewcommand\.[1]{(#1)}
%\DeclareTextAccent{\.}{\UTFencname}{"02D9}
\begin{document}
\.C \.a, \.w \.W
\fontencoding{OT1}\selectfont \.w
\end{document}
fontspecloadxunicodeso it is quite possible that documents which didn't loadxunicodebefore change. – Ulrike Fischer Nov 24 '11 at 09:07