Lightroom works perfectly fine with layers for me. Lightroom looks at the layered image as though it were a flattened file, in other words it sees the cumulative effect of your photoshop edits. The full photoshop file is saved on disk, layers intact. If you want to go back and edit the layered file, just make sure you choose "Edit Original" when choosing to edit out of lightroom. That will pull up the full layered photoshop file.
If you want to use lightroom to add additional edits to a layered photoshop file, that works perfectly well. Lightroom doesn't change the underlying file, just keeps a record in the LR database of what edits you wanted to apply to it. So you can go edit the underlying layered file and it won't effect the LR edits that you've applied.
For example, I'll work up a multi-layered final edit file in photoshop. I'll then use lightroom to handle cropping, sharpening, noise reduction, etc. Sometimes I'll even change my mind after an edit and use lightroom to change global things like brightness or warm up the white balance. If I want to export the photo for web or print or whatever, that comes straight out of lightroom. However, the uncropped unsharpened image still is on the hard drive. If I want to change it, all I have to do is choose "Edit Original" and I can go back to the source file and edit any layer that I want. The lightroom edits will still be there, and will apply on top of whatever work I do in the Photoshop file. So I wouldn't want to warm up the image in LR and then go back into photoshop and also warm the image, since both edits would be applied.
Here's a real world example... I had a large multi image composite that I had finished. I saved the composite as a layered TIF file. I then used Lightroom to open a flattened copy (Edit a Copy with LR Adjustments) into photoshop and started with a fresh "base layer" to build my curves/saturation/dodge/burn adjustment layers onto. I saved that Layered TIF as a second file. After going back and looking at it, I could see that I had made an error in the initial compositing phase of the image. All I had to do was choose "Edit Original" on the composite image and I could fix my error on the layered TIF. I then exported that as a new flattened layer (either Export, or Edit a Copy with LR Adjustments) and then pasted it in as a new background layer in the second "final edits" image.
All this to say, I think that LR works perfectly with layered images, allowing me to access the original layered file when I want to (Edit Original) or start with a flattened clean slate when I want to (Edit a Copy with LR Adjustments). The middle option (Edit a Copy) keeps the layers but builds a copy if you don't want to touch the original file.