Well...it's only been a year.
Finally decided to rummage around and see if I could make this happen myself...turns out it was easy as pie.
Make the simple change(s) below, and next time you run BPP, it'll create a subfolder under "calibrated/light" named by the filter e.g. calibrated/light/Red. This allows you to calibrate all your light sets at once, and keep the calibrated results nicely sorted by filter.
1. Open BatchPreprocessing-engine.js either in PI's script editor or your editor of choice
2. Find (in mine it's line 1647) :
IC.outputDirectory = File.existingDirectory( this.outputDirectory + "/calibrated/light" );
3. Change to :
IC.outputDirectory = File.existingDirectory( this.outputDirectory + "/calibrated/light/" + filter );
4. If you also wish to sort your calibrated flats by filter, find (in mine line 1633)
IC.outputDirectory = File.existingDirectory( this.outputDirectory + "/calibrated/flat" );
5. And change to :
IC.outputDirectory = File.existingDirectory( this.outputDirectory + "/calibrated/flat/" + filter );