I'm sure your shipping dept doesn't want to ship to invalid addresses because they're simply skipping line 2 which might contain the actual suite number or important delivery instructions, right?
Zen Cart is merely collecting the complete data. It's your shipping department that doesn't seem to want to use all that data, right?
Why not change your shipping/fulfillment systems to put both lines onto one before printing the shipping label?
When you've got "Address line 2" set to "false" as you indicated, then this has nothing to do with any "autofill", especially not by any browser ... since the "line 2" field is never even presented to the browser in that case (thus it could never be auto-filled).
So, that then leaves the idea that it's being filled in with data from the customer's actual address as on file at PayPal when the customer uses PayPal to create their account on your store.
You have a few possibilities to deal with this:
a) Turn off the EC Shortcut Button in your ZC Admin PayPal EC module settings. Then customers must create their account on your store before commencing checkout, thus creating their address in your store first.
b) Write custom code to tell your shipping systems to take both pieces of data and combine them into one line, so that you don't get stuff shipped back as undeliverable.
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