Why use 東京大阪 as examples? They are compulsory stops.
HSR stations are independent from the old lines anyway.
As long as there is a passing track and there is no sharp curve near the station, trains can pass through at 300+kph.
Cost is the primary reason for China to build HSR stations out of town. It costs too much to acquire urban land and demolish buildings to make way for straight route and huge stations. Having said that, the distance from the city is way too far for many HSR stations in China. For example, Wuhan Station can be built much closer to the city, without penetrating through built-up areas.