Hmm, yes, this thread is getting a little confused.
One of the reasons for the creating of 'disk images' was to allow emulators to use the image as a virtual disk. So the image file needs to be able to be read/written to just like the real disk.
The use of images for data retrieval/archiving can be somewhat different.
My understanding is that the image created by the flux readers cannot be used by other software directly, I believe that it is normal to create the flux image and then convert it to a normal image that can be used directly.
'Normal' images cover a wide range of complexity, from the simplest (raw data, i.e. sector data only, no format information) to formats that CAN cope with a large range of 'oddities' in the format and hence contain a fair bit of format data, and flexibility, and may well be able to cope with the example quoted, i.e. some tracks at one format, other tracks with a different format. Dependant on the abilities of the FDC or course.
The HFE images are just a 'normal' image of sector data, but a fairly complex version that CAN code with some format oddities. HFE is the default image type for some Gotek setups, but it is possible to config a gotek to use other types. For example, I'm involved with Amstrad conputers, CPC and PCW, and here a .DSK image is used with emulators and Goteks, the basic .DSK being fairly simple, but there is also an Extended version which can handle more oddities.
Yes, it is possible that a raw image file might be read directly by boot ROM, as there is no other data in such a file, but it would be difficult to be sure that the data was in the right place in the image to be read normally. Emulators of course would need to do that, emulators for the PCW computer do boot from a .DSK image file and I'm sure other systems (emulator for computer X and image file for the same computer) will do the same. Using a raw image makes this easier, but not necessarily easy.
A while back I was looking at a process to convert HFE images to something like .DSK but the HFE image was more complex than I liked. I was looking at the HxC system but again it was much more complex than I needed.
Geoff