The boss style death is determined by the monster stats. You'll need an editor to tweak those.
I recommend my Monster Plugin
. It has labels for the some settings that other tools don't. Unzip the DLL into the same directory as Temporal Flux, and you can access it from the Plugins menu. It's still a bit of a work in progress, so let me know if you have any problems.
At the very least you'll probably want a full set of immunities, HP 1/2 and Death Fails, Boss Death Animation (this is the one you specifically mentioned), and SightScope/Relic Fails.
For the event question - you can't determine the status of anything outside of the current location. You'll need to compare a RAM address that was set by the game. The Frog King is after getting the Masamune, so we can find a plot point pretty quickly.
Do a comparison, Value-to-mem. The Address should be 7F0000, known as the storyline counter. Chrono Trigger uses it to track the plot. The Value should be 84, which is what it is set to after the flashback. The width is one byte, and the operation is ">=". Update the command you'll have a condition that triggers properly.
Knowing useful RAM addresses will really help. Temporal Flux has some labeled after updating, but the Chrono Trigger Database