Yes, this is the intended behaviour. If you don't like it, then, as a workaround, you could try to clear the variable called "sage_configurable_latex_macros". YMMV, but this works for me in a fresh sage session:
sage: from sage.misc.latex_macros import sage_configurable_latex_macros
sage: global sage_configurable_latex_macros
sage: sage_configurable_latex_macros.remove("\\newcommand{\\Bold}[1]{\\mathbf{#1}}")
If I now type "html(x)", then the result is "<html>\[x\]</html>", instead of "<html>\[\newcommand{\Bold}[1]{\mathbf{#1}}x\]</html>".
If that gives errors due to a bad definition of "\\Bold", then maybe you should also do:
sage: sage_configurable_latex_macros.append("\\renewcommand{\\Bold}[1]{\\mathbf{#1}}")