OK, this will be my last comment, as I do not know this stuff for a fact, I am summising based on my general system knowledge
Firstly, CPU is not necessarily linked to disk/IO usage. That is, an application that accesses the disk a lot does not necessarily generate a high CPU load. A program doing a virus scan, uses lots of disk because it is reading all files on a file system, it then uses lots of CPU because it is processing the data and applying CPU intensive data matching and heuristic routines to the data. An application that is copying large amounts of data from one place to another (eg: Windows Explorer) generates less CPU for the same amount of data as say the virus scanning app.
So in this instance you are right, the copy process would not generate enough CPU to get tamed using the current version of PT, but the IO still can make the PC unresponsive to other applications you are running. Hence my suggestion that you could monitor storage IO and have a similar set of storage IO parameters which if exceeded then triggers PT to lower the applications PRIORITY (exactly as now).
Provided you are running more than one application at a time, reducing an applications priority, and hence the amont of CPU it is allowed (or "offered" by the OS), you are doing the same as you suggest - you are "proactively SLOW(ing) DOWN" the application and therefore the amount of IO it can generate, which should/could/may make the system become more responsive to other applications again.
I hope this makes sense