There's a lot more to determining the relative phase of two Tesla coils than the direction of the windings. Even if the two gaps were completely synchronized (which will NEVER happen), consider that if the two secondary systems differ in frequency by any amount (which will ALWAYS be the case), the phase will be out of whack in just a couple of cycles.
But to your question, I don't think there's any hazard to allowing them to arc to one another, and that their NST's are different doesn't enter into it at all.
Regards, Gary Lau
MA, USA