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It is hard to imagine how this can be useful. IIRC tags are unordered, so you could end up with long.fantasy.favourite, fantasy.long.favourite, favourite.fantasy.long, etc. It gets worse if you have more tags. That said ...
Search & replace operates on 1 tag at a time, not the set of tags. There is never a comma in a single tag, so your search/replace does nothing.
To do what you want, you need to use the "template" search field. The template is {tags}, or perhaps in your case {#filter}. This lets you get all the tags as a single value instead as individual values. You then replace COMMA SPACE with PERIOD, as in ", " and ".". Set the destination field to tags or #filter.
Here is an image of the Search & replace dialog.
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