The machining margin is how far outside the geometry outline MeshCAM will take the cutter axis. I usually set margin at about 3/4 the cutter diameter. 3/4 of the cutter diameter leaves a reasonable kerf for clearing chips. Anything more just makes a larger kerf around the part. When you’re using perimeter supports you also want to minimize the kerf to avoid sudden lateral moves into the raw stock when the cutter gets down to the level of the support. That has been brought up in another thread.
On 3D parts with a variable-depth “equator” line, I like to use a margin of just less than the cutter radius. With a ball-end mill, this will machine almost to the edge of the part, and the cutter will not “fall off the edge”. There will be a little cusp to hand-finish but this can avoid a lot of extra machining time becuase the cutter only goes as deep as necessary at each point of the perimeter, rather than a maximum depth that might be excessive for some areas of the part.
Randy