It makes sense to me that disabling the 6Gbps port would lower your boot up time as your machine wouldn't need to initialize the drivers for that port. Not sure if that's really how it works. Since all your drives have SATAII interfaces you could just hook them up to the 3Gbps Intel ports and ditch the Marvell controllers completely.
Lenovo W520 w/Windows 8.1
IBM dx340 (Hyper-V 2012, Windows Server 2012, OpenSUSE 12.3)
Nokia Lumia 928