I’ve never looked at the owners manual for a civic, are they really comprehensive enough to address everything that should be done at the 100K mile point? Just asking, I don’t really know. I wouldn’t want the OP to get the impression that anything not explicitly called out in the owners manual is unnecessary for the life of the car.
I would also seek out a good independent mechanic that specializes in honda (or at least asian cars) and ask his advice, especially if you are interested in keeping the car for the long term.
I agree that the term “tune up” has become meaningless.