Not to defend the patent system too much, my experience with it mostly involves a second parties trying to patent ideas that others came up with, but there seems to be a bit of a selection effect problem here. Of all the people who consider copying something patented, some fraction of them are stopped by the presence of the patent. Of all the people who independently invent something you would expect only a very small percentage to be stopped by a patent. Also, someone who knowingly copies someone else's work knows to hide the fact.
So unless we know what percentage of people were stopped from copying someone else's work without the need for a lawsuit, this study alone doesn't tell us very much about the social costs and benefits of patents by itself. I tend to believe that our patent system is too strong and I might very well mention it in discussions with proper caveats, but we need more research.
This research doesn't tell you much concretely about the benefits of the patent system that might be lost in any potential reform, but it certainly says something about the costs that it imposes right now: clearly lots of people get sued over things they invented independently. In fact, in the overwhelming majority of cases not involving chemicals or pharmaceuticals, the people being sued (and thus punished) are independent inventors. It's hard for me not to conceive of "people getting sued over things they invented/created completely independently" as anything other than a pure cost to society, and the research in this paper makes it pretty clear that most patent lawsuits fall into that category of "pure cost to society."
It also does say something about the "benefits" of the patent system, though less strongly: clearly if the vast majority of people being sued in particular industries are independently inventing things, that means that the knowledge transfer benefits of patents in those industries is likely over-stated by pro-patent lobbies.
So unless we know what percentage of people were stopped from copying someone else's work without the need for a lawsuit, this study alone doesn't tell us very much about the social costs and benefits of patents by itself. I tend to believe that our patent system is too strong and I might very well mention it in discussions with proper caveats, but we need more research.