There have been many complaints leveled against lossy+lossless hybrid audio codecs lately. A lossy+lossless codec is one that codes a lossy layer, and has an optional enhancement layer to bring the quality up to lossless. Some examples of hybrid lossy+lossess audio formats are HD-AAC (MPEG-4 SLS), mp3HD, and WavPack. WavPack and MPEG-4 SLS can also run in pure lossless mode.
Lossy+lossless audio codecs do have many shortcomings. They require a canonical bit-exact version of the lossy decoder. This doesn't align well with modern popular pure lossy codecs. They (generally, WavPack does not) require a completely different coding scheme for the lossless enhancement layer that has similar complexity to a pure lossless coder on its own. They need to keep the lossless correction layers synchronized to the lossy file either on the file system or with special tools to attach and separate them. The sum filesize of both the lossy and lossless content is generally larger than what you would get using a pure lossless coder. All of these things certainly serve as barriers to adoption and good reasons to avoid lossy+lossless codecs should you not need their particular benefits.
The biggest benefit of lossy+lossless is that if you need to have a lossy copy as well as a lossless copy the sum space consumed will be less than having a lossy copy and a pure lossless copy (assuming you are using a good lossy+lossless codec).
The reason you might want a lossy copy rather than transcoding on the fly is for syncing a portable device where the whole library doesn't fit. In that case the user may swap music in and out on a regular basis. Transcoding 72 hours of music (72 hours * 128 kbps = 3.96 GB) well is a slow process, even on a fast machine.
I do recognize that this is a niche use case and that lossy+lossless adds a lot of complexity to the system. As storage on portables keeps getting larger and larger this advantage seems less and less important.
I think if anybody could have popularized such a codec it would have been Apple during the heyday of the iPod shuffle. iPods use a database with a syncing tool (iTunes) rather than USB mass storage making the single file solution an obvious choice. Remuxing on the fly is much faster than transcoding on the fly. But seeing as they haven't adopted lossy+lossless yet, I doubt they will bother with it at all.