Yeah, and I checked Bahamut's AI and Mombomb's, and neither uses those two bits in its transition.
Still, I'd like to experiment with them to see if there's any noticeable effect.
It would be pretty easy to try it out on D.Mist...

OK, so I tried it on D.Mist.
It does something, but it's weird...
Apparently, when you set bit 6 or 7 in the parameters of F0, the command makes the monster flash the second form, but then revert to the original form again.
And it appears that which bit(s) is (are) set determines the duration the second form is visible.
01:a literal flash
10:about half a second
11:about one second
So... Not really very helpful, but somewhat interesting to know anyway...
I figured some of this mystery out!
Those top 2 bits seem to indicate the monster slot to apply the change to. The ones that have it set are those that occur with other monsters in the encounter.
As for the transition style, that is controlled by the [previously] "unknown byte" in the special monster size table, byte 3 (zero based). The bottom 4 bits, specifically:
0 = Instant change, no sound
1 = Pixelizes out one and pixelizes in the next, no sound ***Neato and unused??
2 = Flicker between, play sound effect
3 = Funky scanline transition effect, no sound ***Also neato and unused??
4 = Shake a moment, then instant change, no sound.
5 = Shoot up, then back down, no sound. (Dr Lugae)
I'm not sure what the upper 4 bits are used for, but it is also obviously monster index related, as they are only used on those where there are multiple monsters in the encounter.
So there look to be a couple of extra effects that I don't think are actually used. Some monsters have them but those monsters never change graphics. To see them in the debugger without modifying the ROM, go fight the Mist Dragon, put an execute breakpoint at 02:CCC7, and change the accumulator to any of the values 0-5 above.