Jim, did you try manually entering the same order in X3, so you can see what the pop-up message is?  Is it still because of the inactive customer?  Sage is supposed to have all pop-ups disabled for the sales order when calling from a web service.  The only time I have had issues with pop-ups in V12 is when it's related to an Avalara message.  The Avalara messages don't seem to be disabled for web service calls for sales order entry.  We had one client where we actually had to modify the standard code to suppress the Avalara messages during a web service call for order entry.  

I get the same 'field error: sold-to - inactive customer' popup if I try to enter an order for the same customer in both versions. (That's true, the customer is inactive.) 

I wondered what the errors look like on submitting an order with restricted products, something we use extensively. In that case, the array has four messages.

(2-warning) "Do you want to re-calculate the requested delivery date from the current date?   (No)"
(2-warning) "Delivery lead-time is modified : Recalculation of the shipment date"
(3-error) "Prohibited Product"
(3-error) "Field error [M:SOH4]ITMREF"

So, this is at least similar to V9 and still usable.

This is a known issue with V11 and V12.    There was a partial fix in the later versions of Syracuse, which you would also still need to apply, but the fix for the error reporting didn't get shipped until 11.0.17 and 12.0.23 patch sets

Hope this helps