I used a soft 3-ring binder for supplemental instructions. It can be used for instructions in one section and copies of the various IMO documents in another, the two mentioned in this thread to start.
How those instructions are linked into the SMS depends on how it’s set up, some allow ship specific documents without company approval if not than voyage specific instructions / voyage plan or through the standing orders.
EDIT: IMO doc [A.893(21)] is worth reading closely. The berth to berth wording is wrt the “full assessment” not necessarily the track-line. Once the ship stops steering courses and is being maneuvered then track-lines and courses become irrelevant. That approximate / estimated point is where the track should end. This could be put in the master’s instuctions.
As far as not knowing the planned berth a berth to berth full assessment cannot include information that doesn’t exist.
EDIT 2: This IMO documrnt could provide a referance / justification for having irrlevant alamrs shut off ECDIS – GUIDANCE FOR GOOD PRACTICE
From that doc:
16 Unnecessary alarms and indications – feedback from mariners shows that ECDIS can produce excessive and distracting alarms. This is due to a combination of the interpretation of the requirements of the ECDIS Performance Standards and the ENC ncoding. Some control over the number of alarms and indications is available to the mariner in ECDIS built to the revised Performance Standards (resolution MSC.232(82)), but this is not always recognized.
Workaround – the methods available to minimize alarms are included in the syllabus of IMO model course 1.27 on Operational Use of Electronic Chart Display and Information Systems (ECDIS)