"Merge clips" how do you mean? I'm probably missunderstanding ... but the clips in the source sequense should be on different layers, unless they are appear at different times, but they shouldn't "merge" when you cut to a different camera you are in fact cutting to a different layer in the source sequense.
By referring to merge clips I mean the new workflow where you select clips you want to sync in the project panel and right click > "Merge clips."
I wrote that in kind of a rush and the terminology with the new type of sequence that represents a multi-camera sequence (but the icon is different from a timeline and you create a timeline with it that you edit it in using multi-camera editing mode) is a little fuzzy to me.
I think there is bug somewhere though in editing on that timeline you create from the multi-camera sequence... possibly having to do with edits made that are beside the multi-camera ones, like if I use the razor tool and move something. I am going to try to look into it more.