Thanks Svenka - I think I'm confusing terms. To my thinking, a raw image was the data straight from the FDD, with encoding still in place.
The term "raw image" has been used for a very long time to contain the pure sector data without any format information. They have been used in emulation, but also as a way to archive and distribute floppies. For example, Linux distributions (or at least their boot disks) were provided as floppy images which anyone could write themselves for installation; IBM also shipped similar disk images on their OS/2 CD-ROMs.
Since the file itself lacks any metadata, the files do not identify themselves. FlashFloppy on a Gotek tries to identify them by file size and file extension (and allows specifying the format in its configuration file), but this is an inherently inreliable process. This is where special formats are useful and common, often designed and popularized by emulators.
I guess they call them Flux images, though if the data rate is knows, the flux stream for each track should be possible as binary.
While flux images contain all the information and are great for archiving, the files are quite large, require special hardware to be created, and cannot be used for anything as-is. A regular FDC cannot read or write flux data directly. There are other intermediate formats, such as Teledisk (TD0 files), which have been used to archive and recreate floppies to the ability of standard hardware.
I'm floundering here .. What is an "HFE" file and how do I create it?
When I learned about Gotek's a long time ago, HxC2001 was the only useful firmware for those devices. The HFE format has been designed for this firmware, and allows it to handle some oddball formats (such as yours) while still being able to be read/written from the Gotek hardware. It is also supported by FlashFloppy now.
In order to create those files, the best way is to probably follow the step-by-step guide from the original author:
https://hxc2001.com/download/floppy_drive_emulator/HxC_Floppy_Emulator_Software_User_Manual_ENG.pdf
edit: I've looked at the software and can't find a way to easily create a multi-format file. FlashFloppy can specify such formats in IMG.CFG, but I can't create an empty file for you - you'd need to specify the actual format much more accurately. I don't know what system you are trying to use with a Gotek, the format may already be predefined in the tools.