Why "had" was used here [duplicate]

I agree that these are politeness forms that don't seem to relate directly or literally to the standard point in time corresponding to the tense being used. It seems to me that what "I was wondering" and "You had mentioned" have in common is that they soften the statement by moving it farther into the past. "I was wondering ... [but I'm only now bringing it up because it's not that urgent]" "You had mentioned ... [but maybe you wouldn't mention it now, so we don't have to talk about it if you don't want to]." "I thought" for "I think" would be another form that I think fits this pattern: "I thought ... [but now that you have said something else, I might be open to persuasion]."

The past perfect tense is used to denote an action completed prior to some past point of time specified or implied.

She had gone by then.
When Sheila returned home, Mark had been in his room for 10 minutes.
When they arrived we had already started cooking.
He was very tired because he hadn't slept well.

In all these sentences, the past perfect is used for an action that is completed prior of the other actions (to start cooking was already complete before they arrived).

The use of the past perfect is not limited to some verbs, or a category of verbs.