You can install Workbench 3.1 with Kickstart 3.0, IIRC. Issue is, you don't get the full benefits of 3.1. Remember, 3.0 released WITH the 1200/4000 and first release of anything, though this was also a continuation of Amiga OS, is not necessarily free of bugs. 3.1 was a lot more compatable with older software than 3.0 was. Not to say it was in any way fully compatable. Any game that has issues with systems faster than a 68000 has nothing to fall back on in a 1200 which comes with the 020. This was why most accelerators for the 500/2000 had an ability to be switched off and why the 3000 was looked down on by some Amiga owners though it was a MUCH better system than a 2500 with like processor and HD controller.
HOnestly, to play games you dont need more than 3.1 ROMS and workbench. You dont need 3.9 and wont be using anything it offers most of the time.
It is mentioned that the 3.1 ROM had bugfix improvements and RTG improvements over the 3.0 ROM. I dont recall what other defeciencies you have running 3.1 workbench with 3.0 ROMs but there was something.