Looks like you want to be able to get the stations of each subway line (Red, Green, Blue, Orange) exactly as they are presented to the public.
A GTFS stop could be a station, a platform, a station entrance or exit, a boarding location, or even any generic location within a station. It is important to note that the GTFS stop data structure does not contain any route information.
Also, your query above does not return any route data. The MBTA documentation states: "Note that route can only be included if filter[route] is present and has exactly one /data/{index}/relationships/route/data/id." That is, you'll get included route data when you're asking for the stops on a specific route.
So to get what you want, you'll have to first ask for routes of type 0 and 1, and then ask for the stops of each route. When you get all the stop objects for a route, you need to cast out those you aren't interested in. When looking for a top-level station, I check for a null parent_station field. NOTE: There is a location_type field in the stops query, but I've had trouble using that as a filter.
Other things to be aware of: The Mattapan Trolley is a separate light-rail route (not part of the red line). The Green Line is actually comprised of numerous routes. The Red Line is one route even though it has two branches. The Silver Line (all variations) are bus routes and will not be found in a query for route types 0,1.
Hope this helps,
Drew