理由としてはもっとも単純には、主節が have -en だからだろう。
現在まで続いている事象の出発点を、had -en という「過去の過去」でわざわざ言うこともない、と言えまいか。

.... since S had -en をコーパス検索すると、主節も過去完了であることが多い。

He had traveled extensively in the years since he had left England.

Fifty-seven years had passed on Beau Soliel since he had left on the Mary Damned.

it had been so long since I had seen you do that.