Are there any differences between MacPro4,1 2009 and MacPro5,1 2010 besides firmware? I've noticed on many used MacPro listings that people have upgraded a MacPro4,1 (a.k.a. 2009) to a MacPro5,1 (a.k.a. 2010) simply by updating the firmware. From this, it appears that these machines are now able to accept 6-core Xeons as well as utilize 1333 MHz DDR3 RAM.

While this sounds all great and magical, is there anything else that changed between the two revisions of the tower? I'm asking more along the lines of physical rather than software; i.e. is a 2009 model with updated firmware inferior in any way whatsoever to a 2010?

UPDATE 2015-11-02 just to be a bit more specific, my curiosity is more around if the 4,1 and 5,1 are identical except for the upgraded firmware and new CPU/GPU options? Considering the CPU/GPU can be replaced aftermarket, I'm curious if (say) the motherboard is identical between the two revisions or were there any modifications?
The Mactracker app (for Mac and iOS) is a great resource for questions like this. You can check out all the specs for yourself side by side, but the more significant differences are:

4,1:

Processor:          Intel Xeon 3500 or 5500 series ("Bloomfield, Gainestown")
Graphics Card:      NVIDIA GeForce GT 120 or ATI Radeon HD 4870
Graphics Memory:    512 MB GDDR3 (GeForce GT 120) or 512 MB GDDR5
                    (Radeon HD 4870)
Display Connection: 1 - Mini DisplayPort and 1 - dual-link DVI




5,1:

Processor:          Intel Xeon W3530, W3565, W3680, E5620, 
                    X5650, or X5670 ("Bloomfield, Westmere,
                    Gulftown")
Graphics Card:      ATI Radeon HD 5770 or ATI Radeon HD 5870
Graphics Memory:    1 GB GDDR5
Display Connection: 2 - Mini DisplayPort and 1 - dual-link DVI