GIMP should be able to handle JPEG data as-is as "JPEG layers". They would only 
allow lossless transformations (e.g. rotation at 8x8 boundaries) until they are  
(maybe automatically) converted to "normal" bitmap layers.

Why this is useful:

. You could open a (non-GIMP-created) JPEG file (which contains a single JPEG 
layer), add an alpha channel, and store the result as a JNG file without losing 
information (that was not already lost in the original JPEG).

. It would be possible to create and handle MNGs with multiple JNG streams (this 
would require in-GIMP conversion of layers to JPEG data).

. You could add another non-JPEG layer on top of a JPEG image, store the result 
as a MNG or do re-quantization in GIMP when combining the layers (and only 
changing the JPEG data where it absolutely has to be, retaining the image 
quality in unchanged areas).