Suppose mana produced by Boseiju is spent on a spell and an effect creates a copy of that spell. The copy can be countered, even though the original can't.

The spell can't be countered if the mana produced by Boseiju is spent to cover any cost of the spell, even an additional cost such as a splice cost. This is true even if you pay an additional cost while casting a spell "without paying its mana cost."