Beijing/Shanghai have yet to demonstrate the level of innovation that comes out of the Hong Kong/Shenzhen connection.
And, parents still send their kids across the border in mainland China to go to school in Hong Kong.
China may have opened up, and is continuing to open up more, but by no means are the gates fully open at Shanghai. Innovation still primarily comes from the south and regions that are farther from the federal government's base.
Secondly, most innovations happen in Beijing, you can count whatever stats you like, such as # of patents filed, high tech start up numbers, VC funds and where they invest their $ etc. You'd be seeing more than half are in Beijing.
To give you a very quick example: Xiaomi, Didi, Mobike and OFO are the 4 unicorns of China's internet industry, all headquartered in Beijing, their R&D are done in Beijing, these four have not gone IPO and the youngest worth $1B.