I am answering myself because I just came back from this transit in Shanghai Pudong.
Immigration obviously does not close, however, the desk/counter that gives those permits of 24, 72, and 144 hours in immigration was closed. For that reason, you are asked to pass to the normal "VISA" immigration lane where other immigration officers will manage your case.
The procedure took about 20 minutes to get the VISA-FREE-TRANSIT stamp and they just requested my outcoming flight e-ticket and the filled arrival blue card that I picked up from the VISA-FREE-TRANSIT lane that was closed.
IMPORTANT: Do not throw the departure card (that comes attached to the arrival VISA-FREE-TRANSIT card), since in your departure you need to submit it and I didn't see it in the departure area.
For this ~35 hours transit they gave me the 24 hours transit stamp.
I hope this info remains useful for other people.