I stumbled across a work around on the overlapping item issue. If I go VIEW - SHOW SEARCH RESULTS the overlapping items return to the old side-by-side behavior. As long as the search results pane is visible my events with the same time or overlaps show side-by-side.
Yeah, I noticed both things that you are talking about. I don't have that many things in my calendar that overlap, so I can probably live with it. I also noticed that if you change the text size, the overlapping also disappears if you make the text big or small enough. The other thing that I've seen is that the overlapping usually happens when two events coincide, where one of the events falls on a time that isn't on a 5 minute interval. I don't know why this is the case, but it is in my experience.
I would prefer that overlapping or side-by-side be something that could be chosen in the preferences. I'm not really sure why Apple has it set this way. I do not like it though.