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Then the excessive energy that has to be disposed of during the velocity change generates radiation? Is this true of all mediums? When light transitions from water to air to space does it accelerate? Where does it get the energy to accelerate? Does it absorb it from the medium it is leaving?

IIRC, light doesn't actually "slow down" in a medium like water, it just takes longer to pass through it because it makes multiple short "pit stops" along the way, but still travels at the same constant velocity between stops.

The speed of light in a medium is related to the refraction it undergoes per Snell's law and the speed is inversely proportional to the index of refraction. It is not internal micro- or pico-reflections but the quality of the medium to sustain the wave characteristics of light that slows light down. The slowing of light to a foot a second in Bose-Einstein concentrate is due to the index of refraction of the medium being very high. The index of refraction of a pure vacuum is 1.0000 . . . by definition. If the index of refraction is negative then the light would go backwards. Of course, what the ultimate reality might be probably can't even be guessed.

IIRC, light doesn't actually "slow down" in a medium like water, it just takes longer to pass through it because it makes multiple short "pit stops" along the way, but still travels at the same constant velocity between stops.

Actually, the velocity of light in a medium is slower than c. Light is essentially a transverse propagating electromagnetic wave. Material is made of matter which has certain electromagnetic properties. Even in a non-absorbing medium, the light will experience the eletronic effects of being in this material. I know the physicists on this board will object, but the electronic environment acts as a sort of resistance (just an analogy) and that's were the role of permittivity and permeability come into play. Even though the speed of light is slower in a medium, no energy is lost. The photon has the same energy content. TO conserve energy, the wavelength of light decreases (i.e. increases frequency). The wavelength in a medium is the wavelength in a vacuum divided by the refractive index of the medium. When the light re-emerges from the medium, it's speed again become c and it's wavelength returns to that which it was before entering the medium.