All reports I have seen suggest that once a MacPro4,1 has had the 5,1 firmware installed it will behave just like a genuine 5,1 and this includes esoteric things like CPU chip upgrades.
The one thing I can see to still be concerned with is that the MacPro4,1 as standard uses 'lidless' Intel Xeon chips and not the lidded CPU chips used in the 5,1. Being lidless in the 4,1 they are not as 'tall' as the lidded chips used in the 5,1. So if you tried fitting a faster lidded chip in your 4,1 which would be possible now you have the 5,1 firmware you need to be very careful not to tighten the screws of the heatsink as much so as to avoid crushing the taller/thicker chips. (Theoretically you could remove the 'lids' but this is a very fiddly/difficult task.)
Regarding WiFi as mentioned by Grant, the 4,1 and 5,1 use the same Apple WiFi cards. As a result the same unofficial WiFi card upgrade is possible to add 802.11ac and Bluetooth 4.0LE support. See - https://www.osxwifi.com/product/mac-pro-2009-41-and-mac-pro-2010-2012-51-apple-b roadcom-bcm94360cd-802-11-a-b-g-n-ac-wit…
Since it is the same upgrade for both a 4,1 and a 5,1 I see no issues. Even if you had used a different type of upgrade e.g. a PCIe card or a USB adapter these would behave identically in both a 4,1 and 5,1 model and the only issue with them over the above osxwifi upgrade is that they might need newer drivers if you upgrade to a newer version of macOS.
