Unfortunately despite deleting flags and the mgv6_np_cave section before loading the world (so my flags were: mg_flags = trees, noflat, light), they were restored and activated on entering the world.
Thus my map_meta.txt was modified by minetest to include:-
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mg_flags = trees, caves, nodungeons, noflat, light
mgv6_np_cave = {
flags = defaults
lacunarity = 2
octaves = 3
offset = 6
persistence = 0.5
scale = 6
seed = 34329
spread = (250,250,250)
}
I had no mapgen mods active, which means it's done by the engine. However under the mapgen precendence http://dev.minetest.net/Mapgen_Parameters, it says hardcoded flags take precedence over all others, would would imply there is no way of modifying them (which doesn't make any sense)...