I don't really know eclipse preferences files, but with IntelliJ, those files are OS agnostics, which means that it won't ruin your portability. Unless you define libraries with a full path to your system (That would be pretty dangerous/stupid).
When you share preferences, you're sure that everyone will work with the same conditions on the project (plugins configuration, encoding, profiles [for intelliJ]) which can really be a good thing.
It doesn't bother me when some Eclipse files are here, and I think it shouldn't/doesn't really bother other developers when some hidden files just lay there.