There are also other profiles for the Fuji film simulation modes.
I had another look at Aperture - what it actually does is have an attempt to rectify the underexposure during the import. Sometimes it gets it right, other times not.
The other raw converter I was talking about is the one provided by Fuji themselves. I can batch process in that and then import into LR, similar to what I had to do with a Sigma DP Merrill.
Or I can create some basic LR presets - but I think the simplest solution is to stick to DR100 when I shoot RAW.
Thanks everyone