I'm afraid the HDToolbox in OS 3.1 will have issues with you HDD's; you know anyone who can format and partition them first (using OS 3.9 + BB2 or OS 4.1)?
After that they should be OK; I don't know about your GVP ROM version, but 3.1 will see them as regular hard drives. I boot into 3.1 or 3.5 to mess with WHDLoad on my A4000 and the A4091 could care less. The GVP VER 4.15 on my A2500 does fine with >4GB CF cards under 3.1 but they are formatted in OS 3.9 BB4.