I think it would be nice if wildcard tags defined as interesting or ignored by a user would recognize synonyms.
I'll use an example from the Gaming site: [nintendo-wii] and [wii] (These are obvious synonyms, and have already been merged.)
Now say I want to have all questions related to Nintendo platforms marked as interesting. I would use wildcard [nintendo-*]. It is my understanding, however, that this wildcard would not affect the [wii] tag, although it does have a matching synonym.
It's really irrelevant -- any significant synonym will be auto-corrected and enforced. So there will be no questions tagged [nintendo-wii], as any time it is entered, it will be force-corrected to [wii] behind the scenes.
(yes, for less frequent / uncommon tags what you describe is possible, although rare -- but for a top level tag like [wii] this problem will not exist.)
This could make things a bit confusing for users, but when I look at the list of synonyms (SO) I can't find an example where this could result in unwanted/unwarranted highlights and ignores.
This said, this may still not be feasible on performance grounds. Highlighting and ignoring happens entirely on the client side via Javascript. Checking for synonyms would require more database hits per question page load.
The only technically effective way I can see this happening is by having a "synonym manifest" JSON file that can be put under a reasonably aggressive caching policy and only be loaded by users avid enough to have ignored/interesting tags.
A real problem with this is that not all tags have synonyms that can be used for matching purposes. Take the [gamecube] tag. Since there never has been any question being tagged [nintendo-gamecube], this synonym cannot be created.
This means that you cannot really use synonyms to extend interesting and ignoring patterns reliably under the current implementation of tag synonyms.
I was intending to make a suggestion myself related to this but you got to it first.
The tag synonyms work great for linking intimately related tags together. Great so that we don't have many redundant tags throughout the site.
But as for the interesting/ignored tags, this wouldn't be too beneficial. It would only apply if there existed a tag synonym with a certain set of words (and possibly in a certain order). So for any set of tags for this to work, it would require a "root" prefix with other prefixes for other subgroups. This will clutter up the tag namespace quickly. This might be a good thing but what about the possibility of a tag belonging to a number of groups. Then we would see tags like [root-grp1-grp2-...-name] en masse which is IMHO excessive.
I was writing my suggestion for an alternative system here but I want more time to write this out and make my case. In summary, introduce a tag hierarchy to complement the tag synonyms (possibly even replace it if done correctly). Similar to a type hierarchy in OO. This could easily capture all related tags into one parent tag as well as introduce "interface" relations. e.g., a {scripting} group for scripting languages. These groups wouldn't be usable tags on questions, just for interesting or ignored listings or searches.
