The main difference between those two ROMs versions is the ability to install larger hard drives (> 4GB) through the scsi.device which you cannot load it with 3.0 ROMs.
On the other hand, various bug fixes introduced since the previous version, support for CD32's custom chip Akiko (chunky2planar) and the introduction of 2 new datatypes: ANIM and CDXL in Devs directory.
Although you can install Workbench 3.1 under 3.0 ROMs, it's not completely recommended, as it might look and load ok, but there is the probability that your Amiga will not be stable due to some library functions executed.