The hoods are there to prevent the spread of fire between spaces normally separated by fire-rated partitions. Part B of the Building Regulations refers. In the situation you mention hoods are academic as this is not a fire-rated partition, but a better solution in any case would be to use fire and acoustic rated downlights.
However, the Regulations also cover the requirements for thermal insulation, passage of moisture, ventilation and conservation of fuel and power, among other things. It's all very interesting.
If you surround transformers with thermal insulation they will fail rather quickly. There's also a good chance that the cables on the secondary side of the transformers will overheat, melt their insulation, short-circuit and destroy the transformers. So ELV (12V) may not be an option anyway, if that is what you meant by 'low voltage'.
If you push the roof insulation away from the holes from below, you have no control over where it ends up and you may impede the free flow of air that ventilates the roof space. This could lead to condensation forming on the now much cooler surfaces that does not evaporate away as it should, potentially reducing the life of the flat roof. In any case you will create cold spots on your internal ceiling surface which could encourage condensation, possibly mould.
If you must follow the herd though, use fire-rated, canister downlights with compact fluorescent lamps, not halogens. The heat build-up is not so much as an issue with these and you can probably get away with the insulation lying directly over the top of them. (But I still wouldn't install them in the first place.)