Would merging advanced tag descriptions and tagging tools make sense?
I don't think so. The only advantage you'd get from it would be saving a metadata.json file read and including a qa-plugin.php file. That does not even pay the effort of merging them.
I was thinking of merging them into one plugin and adding some additional functionality I need. Are there any reasons for not doing so?
The fact that there is no real advantage from doing so should be more than enough. Anyway, there are reasons not to do so too. If you merge both plugins then you will have trouble whenever a new version of those already existing plugins is released. Also if you require any support in the forum saying that you're using "X and Y" plugins is not the same as saying you are using a custom plugin that nobody knows about.
Regarding the "additional functionality" then you have 2 options that should avoid some of the conflicts I mentioned before. The very best approach would be to add the additional features as a third plugin, in order to share the code base of the original plugins and easily merge new updates. The other approach would be to extend those plugins. Sometimes there is other approach than the latter but, still, it simplifies merging future releases of those plugins into your code.
Is tag-synonyms functionality not covered in tagging tools via the replacement of pair words?
It is usually better to avoid question in a negative form :) Regardless of that, I don't get the question. Tagging Tools plugin will allow you to configure pair of tags (words) so that whenever a tag is input their replaced form (if any) is used.
does it allow for regular expression replacements?
No, there are just key => value replacements. The matching of that regex you're mentioning should be:
Anyway, changing the plugin code to apply regex matches shouldn't be too complex.