Hi Nate and thanks for this option as well. I did not realize you posted another comment or would have answered sooner. I am not sure if that would help as it would run in 4x where as my GPU's run at 8x. But hold a second...I came to ask advise in expectation (hope) you would see my new comment on an alternative use of the Samsung 950 Pro NVMe, since I already have it. If not mistaken I paid a whopping $499 for it and sitting here unutilized.
The advise I was to ask is if I could turn on and off 1 of my GPU's randomly when I needed to run a task on the M.2, but still keep all 3 physically connected. Either by windows or UEFI. The scenario I require this for is for cloning, imaging and back up to the M.2. I do not have an external SSD (or Cloud software) currently and thus no means to compete those tasks. A quick note, I then re-read your comment and noticed you wrote this 3rd slot is PCH controlled, not something I realized.
I am running into this exact scenario as we speak because I would like to have a dual operating system. I have windows 10 on one SSD and Ubuntu (for privacy) on another. A day or two ago I loaded Ubuntu on my 2nd SSD and installed a private email service on it. I now have no back up of either OS. I am not asking for advise on this dual operating system or wanting you to waste your time to set up a complicated system to perform this. Simply (well maybe for you not me) is can I have 2 GPU's and M.2 physically installed and when I need to back up my system, disable 1 of the GPU's and use the M.2. Thus utilizing only 4 out of the 8 lanes of the disabled GPU. I should also add my GPU's are water cooled and the reason I can not take one physically out to do this.
Lastly I have tried to perform this before reaching out to you and this community and have failed. It appears once a GPU card is inserted, whether enabled or disabled, the system recognizes it is installed and those lanes are unavailable to use. I hoping I am wrong but it just could be my asus hero 7 board does not allow this. Hope I have not complicated my query as I often do. Thanks to anyone that wants to comment.