This requires "normal" Momentum stackup definition - except for the through silicon vias. These TSV need to be isolated from the conducting silicon substrate by some vertical oxide, and that is not possible with normal Momentum vias. But from what I have seen, Keysight have added some TSV functionality for Momentum in ADS2015. You should contact Keysight support and ask for more information on TSV simulation in Momentum.
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Wait ... I see that vias and conductors are both embedded in silicon, with only a thin oxide layer as isolation. That is a lot of area and the capacitance is more critical then, compared to normal TSV cases. I don't know if the TSV approach in Momentum is accurate enough for this case. You should consider using the ADS 3D FEM solver instead of Momentum.
The oxide layers could be auto-generated from the Metal layers by using "derived layers". I had shown the use of these derived layers for auto-generating passivation here:
https://muehlhaus.com/support/ads-application-notes/ads-fem-3d-passivation