Are you using WhateverGreen + agdpmod=pikera boot arg? This is required if you use WhateverGreen and boot only with the 6900XT. I haven't yet tested with a second GPU installed but I would imagine that the presence of the 6900XT means agdpmod=pikera is required then too.
Another option is to switch to MacPro7,1 SMBIOS and boot without WhateverGreen. However I found that that caused problems with connecting to the USB-C connector. Without WhateverGreen, I often got no picture to a monitor connected via USB-C to DP. With WhateverGreen + agdpmod=pikera boot-arg, the USB-C port works perfectly for me.