Lightroom doesn't support layers at all - but Photoshop saves a composite flattened layer along with the rest of the file, and this composite layer is what Lightroom works on.
When you open a PSD from Lightroom into Photoshop, you're presented with 3 options. "Original" just opens the original layered file, but no Lightroom adjustments. "Copy with Lightroom adjustments" gives you the flat composite with the Lightroom adjustments.
You can't have both.
Personally I think working with PSD/TIFF in Lightroom invites a complete organizational mess, and I only use Lightroom for raw files, exclusively. All RGB files go through Bridge/Photoshop and stay clear of Lightroom. And this is the reason.
I do have other DAM software for organizing and searching, though, and don't need Lightroom for that.