Forums are usually devoted to a single subject matter and the threads they contain relate to that subject matter, unless it's all gone wrong and your users are wandering off topic. Threads belong to their parent forums, so if your board separates posts about kittens from posts about puppies into separate forums, you are never going to see a kitten thread and a puppy thread sitting next to each other within your forum hierarchy. This is how it has always been, it's the basic nature of the discussion forum paradigm.
I prefer using my aggregated forum add-on over stock XF's 'search forum' as it provides live aggregation of multiple forums into it's parent forum, but it does increase the database load which can matter if scrappers are hitting your site heavily
Does this addon log view activity by user somewhere on the backend so you can see what pages users visit and the entry points and paths around your site they take? That could be helpful.