I actually do see a use for the final category of tags
Often I won't know the exact wording that is used when I'm looking to see if a question already exists, so I'll search by both the game tag, and the sub-category tag and then just a single keyword.
For example, I did a search for the Blood on Ice quest in Skyrim before asking for help with itasking for help with it, but didn't find the potential duplicate because the related question was titled How do I find the murdered woman in Windhelm?How do I find the murdered woman in Windhelm? and made no mention of the actual quest name. If I had known better, I could just just filtered for something like "[skyrim] [quests] windhelm"
or "[skyrim] [quests] house"
Of course, not many people think to search that way (I didn't at first), however with the number of questions being asked for some games (ie. diablo-3), I'm starting to find adding a second tag quite useful.
As a side note, if you do decide to keep the tags I wouldn't bother re-tagging stuff. If the tag exists, it helps the question get found in related searches, but if it doesn't, oh well no big deal.