As said, the MCT of 5hrs applies to CAN. Individual ports have their respective MCTs. Certainly, agents in HK will print boarding pass for onward if it meets the MCT of the destination or their internally interline policies.
As for TPE, the transit is extremely simple, no MAAS is required. Just simply do online check-in for inbound, carry the mobile boarding pass and reboard. You can even spare time for the lounge.
Just bear in mind, mainland airport usually require to have printed boarding pass, so turnaround pairs like CX360/381 are a good pair when tickets need to be issued out of PVG. For PVG transit, you will need to first pass thru PVG immigration, head 1 floor up to departures to check in for your return flight, issue a boarding pass and pass thru formalities to the restricted areas again.