You can even choose to have the original RAW file embedded in the DNG. If you wish your images to maintain the ability to be platform independant, then simply use Lightroom's ability to attach metadata to the image or directory: you can have Lightroom save the images as DNG, with the metadata, including changes, embedded in the file. Lightroom does import, but it is not importing or even moving your images, it is simply importing the data about your image, and creating on-screen previews to aid in editing. During the Lightroom Import process, Lightroom will even copy your originals to the directory of your choosing, because it doesn't put images in the library. Lightroom has superior image management capabilities, zero touch photo editing, and will allow you to manage the files exactly where they are, in directories of your own choosing.
Edits and metadata can be written to the image, to a new image, or to XMP sidecar files, depending on what you prefer. The actual images are not stored in the library. Lightroom uses a library to hold the edits and metadata for your images. You can browse, tweak and yes, delete photos within your directory. It will publish to the directories as well. In fact, it won't even touch your photos.
Lightroom actually uses the directory structure you define, and will use it happily. Doesn't Lightroom use a Library? Yes, Lightroom uses a Library, but perhaps not in the way you think.
