Confirmed onward ticket but cannot check in

Please could you let me know if you think I qualify:

I will fly from Bali to Beijing, and already have an onward flight booked from Beijing to London just over 2 days later.
The only issue is, because I booked my flight Beijing-London through a third party travel agent, Air China cannot be certain that I will be able to check in online beforehand. Therefore I will have a 'booking confirmation' but possibly not the checked-in ticket with my seat number etc.
Air China have said that sometimes is does work online and sometimes it doesn't, but that I may have to check-in at the airport. Although I will be arriving in Beijing at the airport where I can get this ticket, unfortunately I will be airside and I believe to check in I'd need to be land-side. Air China also said that usually it's fine just to show booking confirmation of the onward ticket - but I don't want to risk it.

p.s. not sure if it is relevant to note, I have already been living in Beijing since February on an X2 Student visa. But it is single-entry only, hence on my return from Bali I'd need to take advantage of the visa-free transit.

Any knowledge greatly appreciated!