Applying Fiendish or Celestial template to a Skeletal Champion + class levels [DR 5/bludgeoning] do not result in DR stacking.
Other creatures with racial hit dices above 5 get the 5/alignment DR
I suppose in the template class scaling check levels don't count as hit dices, only racial hit dices do.
You've given your own answer. The damage reduction of fiendish/etc. creratures is based off hit dice, and racial abilities that are based off hit dice only count racial hit dice, but never class levels. So, the fiendish skeletal champion is considered to be a 2 HD creature and does not gain DR from his fiendish template.