Further evaluation did shown the time differences between the 3 GPS modules was due to difference in the trigger level setting of the timer/counter and difference in length of GPS antenna cables. After removal of the phase drift due to Rb frequency offset the attached image shows the phase differences of the 3 modules versus a Rb reference. The two ATGM modules are very consistent over a 2.8 hours period. The NEO-7M varies wildly  with phase errors above 100 ns. Possibly due to a somewhat less optimal antenna position. It seems phase variations over time in the order of 10-20 ns are indeed unavoidable, even with a good antenna.
Erik.
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