Scotty in TMP was referring to the antimatter in the storage pods (iirc), in Generations it was the warp core and not necessarily the storage pods that exploded, the pods might have survived the explosion. The explosion in Generations was similar to the one in Timescape, which was also the warp core exploding.
The self-destruct in TSFS would seem to have been neither the reactor, nor the pods, rather a series of explosive charges spread through the primary hull, I don't recall any explosions in the secondary hull, or in the nacelles.
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In TMP DE/SLV there's no description of the self destruct mechanic other than:
"When that much matter and antimatter come together, aye, we will indeed."
Why didn't they blow up the ship in TFF? Ship seized by a hostile force, intent unknown, crew brainwashed and no longer loyal to the Federation. It would be the most logical option.
Because what you call ``ship seized by a hostile force, intent unknown, crew brainwashed and no longer loyal to the Federation'' is what Kirk calls ``Tuesday''.
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