Hi Will,
Well it depends.
1.) Usually if someone talks about an external 50Ohm antenna, he thinks about an normal antenna with parallel, series capacitor and damping resistor, tuned in a way to show 50 + j0 Ohm impedance at 13.56Mhz (system described above - C_ANT_para, C_ANT_series, R_dmp). Such an antenna can then be plugged with any Z0 = 50 Ohm cable of any length to a reader which is also matched to 50 Ohm. Then the load presented to the reader IC should always be the same. Those systems are also used for higher frequency systems ( ISM, UHF-RFID, ...).
2.) If you have a closed system where always the same cable with the same length and Z0 will be used, someone could just follow the normal design flow as described in AN4974 and use the external antenna + cable instead of a PCB antenna. Any change in the above mentioned parameters (Z0, length, cable manufacturer) could result in heavy de-tuning and malfunction of the reader. Small changes might be corrected by using AAT.
Approach 1. can be used in single ended configuration only.
Approach 2 can be used in either single ended or differential configuration by simply connecting the cable + antenna instead of the PCB antenna. You can already try this using the ST25R3911B-DISCO.
BR Travis