When running # genkernel --mdadm initramfs the initramfs file does not include /etc/mdadm.conf which is expected because we probably use some fixed naming. Wouldn't it make sense to automatically include --mdadm-config=/etc/mdadm.conf when running genkernel with --mdadm parameter?
I would expect that if you don't provide the config option we're running with mdmadm --assemble --scan and letting it put together anything it can. I would agree with this if our default config enabled the AUTO flag by default. Otherwise people might be surprised by a regression.
This is documented in the genkernel.conf file. You need to set MDADM_CONFIG= or --mdadm-config. Without the config it tries to auto-detect instead.