It's as simple as ticking a box, hitting apply then restarting the PC.
My 1080 was running in non MSI IRQ 16 before I did this and was sharing this address with the USB root hub which I'm sure isn't healthy, so I can personally vouch that not all cards do not already run in MSI mode.
You need to download the MSI Utility from here http://www.mediafire.com/file/2kkkvko7e75opce/MSI_util_v2.zip
extract the contents to a folder then double click MSI_util_v2.exe and you'll be presented with this
as the instructions show in the image just click on the msi box opposite your graphics card, click apply then restart your PC, then rerun the program and verify if you're in msi mode by the negative IRQ number (mine was IRQ 16 before then -4 afterwards)
you can also check the msi setting in the device manager after the restart
One last thing, if you ever change or update your graphics card driver you'll need to go through this procedure again as it will default back to the standard IRQ method.