Due to the prevalence of dye transfer printing as the premium option for several decades, certain commercial enlargers came with pin-registered carriers and matched punches, at least as an option. There were other companies like Condit which offered retrofit kits for common enlargers. But still, each tricolor neg would need to be superimposed over a lightbox equipped in a registration punch for sake of perfect alignment, unless a precision pin registration system were present in the camera back itself, which was in fact the case with big graphics copy cameras potentially useful for still life shots too, but not so practical to do with field cameras.
Still, quite a few people did it that way, although it was far more common to make tricolor separations from a color chrome or transparency instead, which makes the whole registration process fairly easy if you're equipped with a matched punch, pin-registration contact printing frame, and carrier. I have a lot of that kind of equipment. Finding enough time to do sequential tricolor printing is another story. But the same equipment has been heavily used by me for all kinds of advanced printing controls such as masking for Cibachrome and simultaneous RA4 printing, as well as black and white printing sometimes.