I was not able to duplicate this in current master or in 3.0.9.
In current master using the default data I added an alert message to an item and turned on 'Display copy alert for in-house-use' for BR1. The alert message did display when I entered the copy's barcode in the in-house use screen.
In 3.0.9 on turned on 'Display copy alert for in-house-use' for the top OU. The alerts also displayed in the in-house use screen.
I was not able to duplicate this in current master or in 3.0.9.
In current master using the default data I added an alert message to an item and turned on 'Display copy alert for in-house-use' for BR1. The alert message did display when I entered the copy's barcode in the in-house use screen.
In 3.0.9 on turned on 'Display copy alert for in-house-use' for the top OU. The alerts also displayed in the in-house use screen.