I had to generate my html files into a directory outside the source tree. So I built a little patch for the xilize engine which will do this with a new commandline option (-o or --output-dir and a dir, which must exist). This will set a new config key named _OutputRoot_ to the absolute pathname of the given directory. Missing directories (except the output root) will be created automatically.
Don't know, if the implementation matches your design intentions, but the code is written and may be you want to make use of it. 8)