Your best bet (aside from the script you mentioned) is to try to convert to epub, edit the doc using Sigil to make it look like what you want, and then convert from epub to mobi. You could also use the debug output to grab an intermediate version of the html - the version from after pre-processing, edit that as required, then convert from html to mobi.
I just looked at the source code, the current code doesn't actually seem to include the case of a '.' appearing just after a numeric chapter header. If you open a bug with an example I can see that that case is added to the default preprocessing. bugs.calibre-ebook.com
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