You are rtight, Online Manual is not up to date : it does not include changes for at least to evolutive versions, and possibly some sections are not as explicit as they should be.
But it's a fact that Manual is always the less priority of our (many) tasks, so it's not at the quality level we would like it to be...
But at least it exists, and is quite complete and usefull (I hope so, othewise we would have lost our time writing and maintening this 360+ pages document)
About your question : LDAP parameters should be entered on Global Parameters screen (and so stored in DB)
But if you enter same parameters on parameters.php file, the values in the file will overwrite valiues in the DB.
In parameters file, you should find only few parameters : parameters dor access to DB, log file parameters and possibly enforeUTF8. That's all.
Others parameters should be removed from this file and be managed through Global Parameters screen.
Idea to add feature to test LDAP parameters as been adding in track (ticket #3775)
About secured access to LDAP, it seems possible to use LDAPS, just specifying it on ldap host paramerter : ldaps://host
I did not test it myself by php ldap connector seems compatible and I read a thread where a user did it (saved on Ticket #2157).
We have ticket #3103 to improve LDAP via SSL as LDAPS in deprecated.
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