I understand the concept behind the validation warning but in reality, this just makes more work for the end user. 

I would imagine many pay runs will be processed after a pay date for a variety of reasons, some listed in this thread here. By making the user lodge an update event instead is pointless. It's the same information reported just more steps involved. 

I understand the ATO would encourage best practice reporting for STP but I don't think its up to QuickBooks to regulate this for their customers. 

I'm a BAS agent and have clients that use a variety of different accounting software & I haven't seen this warning on any other software.

The warning needs to be removed as its counter productive to the concept of STP reporting.