Because the candle black soot produced during combustion, drop inevitable black particles from the Candle on the board / skis. On a transparent place, it is now more transparent so dirty, but better than completely black.
For black spots definitely use the black Repair Candles, with brighter things, you can use the transparent and hope not so much with drips. Later during grinding and smoothing (eg with a razor blade) you get still get some residues.