Is it safe to flush the leftovers of the NaOH and plant matter stew down the toilet? Or should the Ph be neutralized with vinegar or something first?

You're all good. Flush away Lye is common in many drain cleaners.

One love

Yep, it's literally sold as drain cleaner. Just be sure it's compatible with your sewage disposal system (e.g., some septic tanks might not like it). And also, if it seems like a lot of the naphtha has remained trapped in the sludge it would perhaps be environmentally more responsible to let it air in a wide pan before pouring. Mind you, the amount is most probably peanuts compared to runoff associated with motor traffic - so you can weigh that up against the safety considerations of having a pan of caustic sludge sitting around in the open. If both of these factors bother you then by all means just add a suitable dash of vinegar before leaving the whole thing to evaporate, at which point you could dump it in the compost or use it as mulch.