Does this apply to the Futaba 9 super series where can can swap from PCM mode to PPM?
It's not just the Tx Matt, it's also a function of the Rx you have. Futaba R129DP and R149DP are PCM only receivers, so you must to transmit in PCM mode. With either of these receivers you're stuck with the shortfalls I described. Futaba R127DF, R128DF and R148DF (to name a few) are all PPM receivers, so you have to set your transmitter to PPM mode and your onboard failsafe devices will work as expected.
It's also worth noting that some PPM receivers like the SombraLabs SL-8 have a selectable built-in failsafe - good if you want to save space and onboard hardware but you have to tolerate the relatively quick failsafe delay as compared to what we're typically used to dealing with.