That video is of Mike Hodnick, not myself. But to answer your question, the timbres are generally a combination of both things you mention. At its core TidalCycles triggers samples, but it also controls the effect chain they go through; you can pattern "clean DISTORTED clean clean DISTORTED" as easily as "kick hat snare hat". And sufficiently high-frequency control of the synths will have timbral repercussions, too -- alternate, for instance, between two constant frequencies sufficiently quickly and you've built a simple FM synth.