I think your best bet would be to either:
a) boot up in Workbench and set the resolution to the same parameters as you're Linux setup and then use the config tool.
The problem is that I currently don't know what mode is generated once the Linux kernel boots. Mind, it's currently text-mode only, so I actually don't understand why it would end up with a resolution the monitor can't deal with.
b) Use native output on Linux and adjust the resolution to one of the comparable modes of the Indivision.
Well, I have to do some more testing.
I tried version 1.0 of the configuration tool today and I am still struggling to get proper modes. I have seen, however, that there is a new version 1.1 available which provides some sane default modes which I will test.
I might also try to get into touch with the guys from Individual Computers. It would be nice to get the Indivision prorperly working both with AmigaOS and Linux since we're working to revive the m68k Linux port

.
Update:
While my screenmodes for AmigaOS 3.9 are a bit messed up now, I can actually use the Linux console at 800x600/60 Hz. Looks I like I need to dig further into the tool and how to use it.
Adrian