You are married until divorced, so you remain the family member until divorced
As the family member you can acquire PR if the EEA national has exercised Treaty Rights for five continuous years and if you were the family member for those five continuous years.
You would need to prove this. This often creates problems if the married couple will not cooperate when separated.
The other thing you are talking about is Retention of Residence.
Correct me if I am wrong, but for this I believe:
The partners need to be married for three years and have spent at least one year in the UK at the time of the legal separation.
You also need to prove the EEA national was exercising Treaty Rights when the Decree Absolute is issued.
The non-EEA then has to exercise Treaty Rights for the remaining 2 years as if he were an EEA national to complete the five years of exercising Treaty Rights to acquire PR.
When PR has been acquired a person can apply for a document confirming that, so they have to supply the proof they acquired it.
See section 5.4 on :
http://www.ukba.homeoffice.gov.uk/sitec ... iew=Binary
In your case, if you have already completed the five years and your EEA national sponsor also met the conditions and is willing to cooperate by supplying the proof she exercised Treaty Rights for those five years, then you have already acquired PR and hopefully will have the evidence to prove this to the UKBA.
It's those five years that count so you supply the evidence for those five years. Once you have acquired PR, what happens after that date is none of the UKBA's business (unless someone is a serious threat to public security). Whether you subsequently apply for divorce or not is irrelevant.
As for automatically acquiring PR, but having to apply to UKBA.
An example: someone can be a British Citizen, but they often require a passport to prove this.
Likewise, someone can have PR, but it helps if they have a document to prove this.
