I decided to test out tag synonyms and favorite tags, so I added threads to my favorites. When threads is clicked on, it opens to multithreading. However, in the question queue, all questions marked multithreading don't have the "favorite glow". I suggest one of two things:
Questions under favorite tags are highlighted client-side, meaning the question list itself isn't transmitted to you with the favorites already styled appropriately. A script on the client-side adds the highlighting to all the questions that match, and similarly fades or hides any questions which are ignored.
Therefore, the script doesn't know what tags are even synonyms of another tag. The favorite and ignored tags have always been completely denormalized. The tag doesn't even have to exist. Bottom line - no server-side checks are ever done on those tags - you can enter whatever you want.
Your only viable solution here is to just use the correct master tag when you realize the tag you entered is actually a synonym.
There is, however, a nice hint that a tag you're selecting is a synonym. In the drop-down box that suggests matching tags, there will be an
(s) where the number of questions using the tag should be - that means it's a synonym of a master tag and you should probably look into that. Note this only works for synonyms which have been merged into their master tag - if the synonym is still used on old questions, it will still display that number.