I've had a few issues with this recently, which has led me here... When you have a Photoshop file with a Spot channel, it works in Photoshop as expected...
The spot channel Overprints the rest of the image (well, the CMYK remains unchanged). This is accross the whole image, Solid areas and transparent areas.
But when it's imported into ID it knocks out all the areas which have transparency.
Could it remain Overprint by default, and it be up to me to mask the knock outs within Photoshop?
OR have a similar option to Object Layer Options which allows control over Photoshops Spot channels?
Asking for a bit much there?!