I’m not sure where I argued to the contrary. The ships in Trek with self-destruct capabilities are all military (or pseudo-military) vessels that are explained as literally having a procedure such as you describe.

In the preferred configuration, the starship undergoes rapid vaporization from thermal and mechanical shock caused by a deliberate release of warp engine reactants. Remote computer system decryption algorithms generate one final set of cascade failure commands, and all engine safety interlocks are compromised. Matter from the primary deuterium tankage and the total supply of antimatter from the storage pods on Deck 42 are expelled simultaneously, producing an energy release on the order of 10^15 megajoules.

If the command links to the engine systems are severed, the secondary destruct system is automatically selected. Ordnance packages are located at key locations around the vehicle, including the antimatter storage pods. These are detonated in concert with intentional overloads of all fusion reaction chambers. The release yield of the secondary system is calculated to be 10^9 megajoules. The secondary destruct system becomes the primary system for the Saucer Module in Separated Flight Mode.