I just have a some of questions regarding the case of separation (Not divorce) & rights of residence, i did the usual search in the forum & on official government sites but it's bit confusing.

First of all, i read that the legal separation means "Spouses living separately are still seen as married in legal terms", does this mean in legal terms regarding immigration laws too?.

Second, as per Article 27 of Naturalization Act "The foreign spouse of a Swiss national who has lived in Switzerland for at least five years, has lived here for one year, and has lived in conjugal community with the Swiss spouse for three years.", it's mentioned 3 years in total but it's not mentioned if it has to be in the beginning of the stay in Switzerland then separated or have to be valid in time of naturalization?

Third, as per the first point, does this mean you can apply for permit C if you been married for +3 years then separated?

You'll find your c permit answers most likely in this thread: Non-EU Permits - a few bullet points.

As for facilitated naturalization, the marriage must be together in order to be processed. In the final stages, you're asked to sign a paper saying that the marriage is stable.

For more info, you might also want to check out binational.ch.