Without knowing exactly what ways the COWOA code breaks normal operation, I can't answer the question for you.
The setting you're referring to only tells Zen Cart to store a "1" or "0" value to the database when it DOES (always) create an account for the customer. The 1 or 0 simply determines whether that account can also be used to log back into the store and check on status of the order. It also determines whether the customer is sent a password in their welcome email to facilitate this ability to login.
As I said, it always DOES create an account. The setting you refer to only tells it whether that account is permanent and allows login, or if it's temporary and used once only.
It does not necessarily work in conjunction with the COWOA addon, and is definitely not "aware" of the existence of your COWOA addon, unless COWOA has made additional changes to make it "aware".
I'm pretty sure COWOA also always creates a customer account record, just doesn't let them login to it.
**Your question is probably answerable as: "yes, setting that to 'no' will not send the customer a welcome email or login password".
**And since that's probably all you were really wanting to know, then that probably suffices.
Question for you: have you tested it on your test site, to see what the impact is? Or are you saying you don't give yourself such a safety net?
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