What is the SA in VFR
There is no such thing, you avoid visually taking into account SERA.5005 Visual flight rules. You may wish to make additional allowance for obstacles in reduced visibility hence the concept of a Minimum Safe Altitude.
What is the SA in IFR
Historically it was one of the UK Rules of the Air which has now been replaced by SERA.5015 Instrument flight rules (IFR) — Rules applicable to all IFR flights
How is it calculated,
(b) Minimum levels
Except when necessary for take-off or landing, or except when specifically authorised by the competent authority, an IFR flight shall be flown at a level which is not below the minimum flight altitude established by the State whose territory is overflown, or, where no such minimum flight altitude has been established:
(1) over high terrain or in mountainous areas, at a level which is at least 600 m (2 000 ft) above the highest obstacle located within 8 km of the estimated position of the aircraft;
(2) elsewhere than as specified in (1), at a level which is at least 300 m (1 000 ft) above the highest obstacle located within 8 km of the estimated position of the aircraft.
What information is contained in the operations manual re an SA (specifically what and where is this information for the DA42 tdi)
That depends upon which company wrote the manual. It is not likely to be aircraft specific.
See also
ORS No 1124