I understand the issues with loading the firmware on startup but it looks like there is driver level support for the 5i25 in 2.5 now. I assume that the driver does not try to load the firmware at this time. I will try it out tonight and see how far I get
In PnCConf, you would need to select the correct firmware that you have on your card instead of the firmware to upload. I don't think this would be a major issue and only need documentation. From what I have read, I think the pin behavior is the same as the other HostMot2 based cards after firmware load.
The main issue I see in getting it to work with PnCConf is the different number of pins per port. Is it possible to have the missing pins there as virtual dummy pins with reserved functions? That way the UI could stay the same while allowing the lower pin count.