I think it depends on what you're trying to do. If you want to spend $50 on a PCIe to SATA adapter, you might see some improvement, but probably not. As far as booting - no difference. And likely no difference with app start up either. As far as app performance, that will depend on the app and the workflow characteristics.
The thing to keep in mind is a similar concept that is often misunderstood: a primary advantage of SATA SSDs is not speed. When both SSDs and HDDs use a SATA interface the main benefit of SATA SSDs is essentially zero latency (especially true in SATA form factor). That is, when the file system requests some bytes, there isn't a delay due to the disk and head moving to the right place to get the data.
So if the app is making lots of I/O calls, but they are easily accommodated by SATA-II, you won't see any performance improvement on PCIe - assuming the SATA bus isn't otherwise constrained. But if the app is making I/O requests for very large amounts of data such that the difference between SATA-II and SATA-III is constraining the request then you could see an improvement.
If you want to see some file system performance improvement, something like HyperXPredator can help. Whether you need it, or can afford it, is for you to determine. But for the most part, sticking a SATA drive on a PCIe bus in a Mac Pro probably won't make much of a difference in performance, if at all. Another benefit is this will free up a SATA port, so you can put another drive in place.