Thanks for your bugreport and sorry for the late reply.

Your analysis is correct, the probability changed for dependent
packages.

However because of the way we seed the random number generator its less
of a issue in a lot of the practical cases. We use the (source package
name, update version, client-machine-id) as the input for the RNG. This
means that in the linux example all packages have the same probability
because they come from the same source package.

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https://bugs.launchpad.net/bugs/1214482

Title:
  Not-grouping dependent packages in Phased Updates changes propability
  distribution for entire group of dependent packages.

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