Flattened = smaller file but no transparency
One layer = transparency option available
Flattened = locked single layer
One layer = movable and scalable within the document size due to the transparency Ronald mentioned.
Just experiment, you’ll find allsorts of differences.
you can’t use the one layer file in Quark
but you can use it in InDesign.
One of my printers said he received an InDesign file with a linked PSD that had almost 100 layers in it. He said it printed fine. Brand X is definitely on its way out.
All that InDesign, sees is the flattened composite of the PSD.
It has no idea how many layers are in a particular PSD file.