Maybe all I'm asking about is recognizing them in existing .psds then. I opened an existing file of mine and it flattened them to "pixel" layers.
I use Smart Objects basically as embedded files. For example, rendering a package, I make the panels smart objects so they can be easily swapped out when packages are updated. I export a .psd of the updated package file, marquee select and copy the new panel, double click into the smart object of the old panel and paste the new art in. Done. The transform remains as it was, but applied to the new art.
Sometimes, I place .ai objects as smart objects that remain editable in .ai later on, but are embedded in the .psd.