Hmm... StoreFile.computeRefFileHDFSBlockDistribution is also calling that, and doing the right thing (in fact that's where I looked as how it's done correctly).
The other place is CompactionInputFormat, and that's also not right (also wrong in trunk).
I think FSUtil should stay at the FS level, and not know much about HBase specifics. In trunk we have HRegionFileSystem, but not in 0.94. Then again in trunk I see stuff like getRegionDegreeLocalityMappingFromFS in FSUtil. What a mess.
I think for 0.94 it's best to fix it in HRegion. I would just remove it, but coprocessor might call it (and currently get wrong results).