past perfect+Since past simple
S1:He became a physicist in 2000, since when he had done research on the molecular theories. However, he decided to abandon his physics career for personal reasons.
S2:He had done research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

Q1: Do S1&S2 mean almost the same with little difference in meaning except grammar structure?

Q2: Is it possible for “Past perfect” to be used carrying the meaning---time period of an action/event with its starting point in the past & ending point still in the past?
or
I should use “had been doing,” i.e. past perfect progressive to emphasize the duration/span of doing research ? →S2"He had been doing research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

ref: https://www.ldoceonline.com/dictionary/by-since-when

Question

past perfect+Since past simple
S1:He became a physicist in 2000, since when he had done research on the molecular theories. However, he decided to abandon his physics career for personal reasons.
S2:He had done research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

Q1: Do S1&S2 mean almost the same with little difference in meaning except grammar structure?

Q2: Is it possible for “Past perfect” to be used carrying the meaning---time period of an action/event with its starting point in the past & ending point still in the past? 
or
I should use “had been doing,” i.e. past perfect progressive to emphasize the duration/span of doing research ? →S2"He had been doing research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

ref: https://www.ldoceonline.com/dictionary/by-since-when

Answer

Compare these:

S1: After becoming a physicist in 2000, he did research on molecular theories. However, later he decided to abandon his career in physics for personal reasons.

S2: He was doing research on molecular theories after he had became a physicist in 2000. However, later he decided to abandon his career in physics for personal reasons.

As you can see, both the simple and the continuous forms can work, and you can use past perfect or past simple when describing the first event. There are three events mentioned: (1.) he became a physicist in 2000, (2.) he did research on molecular theories, and (3.) he abandoned his career. Using past perfect with the second one is not logical chronologically and makes the meanings of the sentences unclear.

"since when" doesn't sound natural to me, and in the link you posted the examples have different grammatical structures too, so I would not use that either.

Answer

I hope that answers your question.  If you'd like to practice speaking, I'd be happy to help you develop a study plan.  Feel free to look at my teaching profile and class offerings and send me a message if you think I can help you.

Answer

Hi Yunhui, S1 is grammatically incorrect. S2 is correct.

Q2: yes. You can have two events in the past. The past perfect event occurred before the event in the past simple: He had completed (past perfect) his research by the time he became (past simple) a physicist.

Hope that helps!