Thanks for the reply. That link takes you to a page showing payment options including Web Pay which I do use for Estimated Tax Payments. Web Pay also lets you specify a Tax Return Payment even though Form 540 does not include a line for it. I’ll plan to designate any additional payments as Estimated Tax Payments. Their system should know that the safe harbor amount has already been paid and not flag any problems.
I just noticed on page 6 of the Form 540 Instructions that Mandatory Electronic Payments are required when amounts exceed certain thresholds. Fortunately those rules will not apply to my case.