I would like to confirm that adding the extra configures indeed fixed the bugs I experienced with the Paypal module and some custom coding.
The issue is that when you add custom code to Zen Cart that interacts with one of the functions, classes or other code that is being triggered by the Paypal module, the configuration settings set in extra_configures/ wil not be loaded when the Paypal module is active.
In my case this lead to a bug that seemed to occur rarely and randomly. I don't get much Paypal orders and the custom code by itself is totally unrelated to Paypal, so it took me quite a while before I even noticed the problem only occured with Paypal orders.
I know it's not very likely others will run into the same issue, but hopefully this information saves someone a big headache :-)