Mitch showed a way to kill BoomBoom that causes a glitch that skips the death animation and goes straight to the world map. For posterity, here's a demo and explanation; the linked video has closed captioning, sorry couldn't get it to embed.
Youtube video
fm2 demo
Mitch originally did this with hammers, which do 1 hp damage for each hammer every frame. Obviously fireballs are way slower, but clearer for demo purposes. Even with hammers, saving time is very doubtful as you need to wait for the proper moment as described below; not sure if there are any BoomBooms where this can save time.
BoomBoom's HP are stored at $7cfa; the value starts at 37 and he normally dies when it hits 32. However, if the 5th and 6th hits are delivered on the same frame, the hp jumps from 33 down to 31 with BB still alive.
Once HP are at 31, you then have to bring them to 0 to kill BB again. If you deliver the killing blow when BB is pausing to swoop ($51c > 0) then when the $51c timer hits zero, you'll exit to the world map. This is because the timer at $51c is used by the game in multiple places, and the game isn't expecting BB to be killed by HP reaching zero anyway.
Achieving simultaneous fatal fireball hits on the W1 mini-boss while $51c is non-zero causes a glitch kill, but the boss just falls offscreen and Mario is stuck on the empty boss screen forever. It's probably the same with other mini's, but might be worth checking.
Bowser uses the timer as well, but seems to die normally regardless of this effect.