In my flying days I've encountered fleeting local downdrafts and very turbulent vortices associated with thunderstorms but never a rain bomb as described here. My experience has been that the unusual and unexpected is a normal feature of thunderstorms, and that few people appreciate how quickly they form and how short their lives are. I've flown through dark and ominous looking storms encountering nothing but rain: in others I've had violent turbulence, hail sufficient to shot peen the paint off the leading wing surfaces and scare the **** out of me. The energy source is usually reflected sunlight from the ground and condensing water vapor in the rising (and therefore cooling) column of air. The latent heat of condensation of water vapor is about 600 times the specific heat, so a little condensing water vapor in the rising column of air releases a great deal of energy, quickly accelerating the whole process. The result is turbulence, violent downdrafts adjacent to the boiling cloud - almost anything can happen.
There was one between Toronto and the Toronto Islands one year while we were out on a pier for a summer office party. It came up very quickly - some of us made it into the nearest building in time - others didn't and were soaked, some were hit by flying furniture, one industrial-size bbq went through a large glass door. Seconds later, the sky was blue and clear to the west of us.