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.
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.