This MB seems to have limitations that aren't made apparent in the manual as with my current setup, TB is no longer working again, unless there is some sort of coding fix that can be setup in CLOVER under DSDT, but all the coding and fixes that are inputted into CLOVER are beyond me as I have yet to dive deep enough to attempt to understand everything. In addition no one on these forums seems to be much of any help when it comes to my problem, I never seem to get any responses when I have an issue.
I have the same setup still, no one says you have to get rid of your m.2 as the board has 3 slots. I just moved my m.2 to the top slot right below the CPU so I I'm using both the top and the middle slots. OSX on one and WIN 10 on the other, I see no need for 3 m.2's if that's what you're running. Unfortunately as I stated there are limitations that aren't stated in the manual as with my current setup running 2 m.2's, and 4 sata drives, TB under OSX thunderbolt no longer works, but as soon as I disconnect 2 of the sata drives, thunderbolt works again, so with my limited knowledge it seems that the TB seems to be sharing bandwith. I cannot remember if this issue is the same in WIN10, I will have to test this theory again but I am positive because as soon as I had hooked up 2 more sata drives TB stopped working. I'm most likely going to get a nas to get around this issue which is rather unfortunate, or I may end up eventually changing MB's moving over to ASUS as there seems to be more support here on the forums for TB as well as hotplug functionality.