Hello New Guest,
I really understand what you are looking for because when I was at intermediate level, I was questioning everything like you and interested in thinking every sentence in detail. Past perfect tense was my favourite.I questioned and thought about its usage for years because it wasn't an existing tense in my native language. I felt inefficient when I didn't use past perfect or had questions about it in my mind. To tell the truth, sometimes I still have. This is because I learn English as a foreign language and I don't have a native spaking environment key which will open the doors of questions so, it takes ,really, years to completely grab the real and accurate usage of something. This goes for present perfect tense and modals too. The thing you should do, if you care what I say, just to be patient. After years, I am sure, you will regard both tenses same even the past simple better in similar contexts as your original question.
One more thing, your thinking too much analytical on grammatical forms of the language may be an effect of your English teacher. You know, they do unnecessary exams and want you to find the right choice and want you make a discrimination between whether to use simple past or perfect though sometimes both can be used. To be frank, I still suffer from this. I am still too analytic.