I don't know of anything offhand which is complete like that, but you can assemble a station using components to allow upper and lower levels. Using the layers, you can place objects and lock them in place while placing others in the same area. This wasn't available in TS2009 when I tried to do something similar back then.
There are many small shops, even storefronts which might be useful. Look for domsarto (It might be Domsarto). His assets are prefixed with DS. He made some storefronts that can be placed on top of other buildings, specifically UK and Irish buildings, but these may work for what you want. Andi Smith, aka andi06 made various platform splines, and to create a lower level, there are various concrete covers used to bury track, and even using a subway station might be useful for lower level stations. I did that for my version so many years ago and it worked quite well. Sorry I no longer have that particular route version available any longer or pictures of it to share.
There are also complete stations made by Alterr (might be alterr) for his U-Bahn Frankfurt route which have multiple levels where the Strassen Bahn uses the lower level while commuter trains use the upper level tracks. These assets are available at TrainzDepot.net