I 100% guarantee you, and if I'm wrong I will send you my nipple in the mail, that Chrono Trigger did not use FM synth.
Like I said, the bells do sound like they were sampled from FM synths.
It's quite hard to tell though because the SNES doesn't use any multi-sampling and the samples are very short. And while Chrono Trigger doesn't have a great FM soundtrack, it is a very awesome example of a game using the full potential of the whopping 64 kB RAM the SNES' audio chip has.
Imagine having to cram all those sounds in there - and having very limited polyphony too. Madness!