Yeah I guess based on the description, you're not meant to weave them. If it's a cooldown though, it means it won't be modified with skillspeed. GCD will probably be down to 2secs or so like with Monks due to Huton, so you'd need 2GCDs worth to do 3mudras+ninjutsu if they have a 1sec cd.
The average potency of the main combo chain is 233, so 2 GCD would be 466 or so on average. Raiton is 360, so that sounds really not worth it. I assume there's going to be more to it. Even if skillspeed affects mudras, it sounds like a DPS loss, unless ninjutsu animation doesn't prevent hitting the next skill, then it'd be close to 2GCD(2.4secs for 3mudras with a 20% reduction), in which case the higher potency would be worth it.