For items that are on backorders, when selected as part of an assembly build on the WO, can there be any default warnings or pop-ups set to alert the user that the component is on backorder?

it does tell you by default that you don't have enough on hand to make this order

where does it tell you this on the WO?

yes when you try to make a WO and have BOM attached to it, when you select the BOM revision it will tell you if you don't have enough

also look at the Material Shortage Report