Ignore overlaping window but not from project settings, but from script

In your project \Advanced\ events\Genaral events , you have OnOverlappingWindows event. There you may create an event handles for this scenario. click for More.... 

But you can not specify where this could be frigged in your test but can specify on which window

Or else if you know where overlapping occurs and estimated time (you said "very very short time") you can set time for wait. 

like this