The rule is nothing about compensation for expenses, its whose responsibility to rebook the flights if the passenger misconnnects due to the delivering carriers fault. The problem here is that the CA flight arrived at a hardstand close to ontime but the OP's MCT was now significantly reduced due to taking a bus. So CA can claim an ontime arrival even though it didn't arrive at the terminal.

also is it possible since CA didn't issue a boarding pass in TPE that AA denied him boarding as he wasn't checked in for his onward flight and was declared a no show in PEK? The OP claimed that he didnt get to the front of the line until 30 mins before the sked dep time and according to AA tariff rules it was too late.

AA WILL
CANCEL THE RESERVATIONS OF ANY PASSENGER WHO FAILS TO
PRESENT HIMSELF FOR CHECK-IN AT THE BOARDING PASS
LIFTING POINT WITH THE APPROPRIATE BOARDING PASS AT
LEAST {X} 30 MINUTES FOR A DEPARTURE TO OR FROM AN
INTERNATIONAL DESTINATION, NOTWITHSTANDING THAT SUCH
PASSENGER MAY HAVE CHECK-IN FOR THE SAME FLIGHT AT
ANOTHER