A DesognSpace file with filters set in <variable-font> lib are ignored. I’m not sure if these filters are supposed to be processed or not, but in Glyphs filters are set on the instances, and variable font instances are mapped to DesignSpace <variable-font>.
The root of this issue is that *InterpolatablePreProcessor takes a list of UFO files as input, so we would need to get the <variable-font> to it somehow and load filters from it in additions to filters set on on the individual UFOs, or should it be done in a different way?