Puff... I'm installing it on two hdf's without problems. One is a System.hdf of CWB39, the other a new one with PFS3DS. You only have to set them to IDE 0.
About the rom version I've got no idea, but better safe than sorry
, although yes, it shoudn't affect at all.
Edit: I forgot to say that I don't use -once started the OS4.1 installation- in the first place the option to setup the HD, but the folllowing to start installing the OS, and I change later -it will ask- the options of the HD; preparing or formatting it.