According to ArchWiki, the ufiformat tool can command those cheap USB floppy drives to perform a low-level format.
Aside from that, while I can't vouch for it myself, since I've only ever used mine to read floppies, archival/forensic USB floppy controllers like the KryoFlux, Greaseweazle, FluxEngine, etc. should be physically capable of it (they do deal in raw flux) and it's just a matter of software support.
The FluxEngine software recently gained filesystem support and supports Greaseweazle hardware too, so its new fluxengine format command may do what you want.
Alternatively, you could see if something like gw erase followed by writing an image of an empty disk would do what you want. (The help for KryoFlux's dtc CLI also lists a -we=2 option to set an erase mode of "wipe" when writing which may have a similar effect to gw erase followed by writing such an empty disk image.)
Both the FluxEngine and Greaseweazle can be had quite cheaply as far as such boards go (you'll still need a floppy drive, possibly cabling, and possibly an external power supply, depending on the board and whether you buy a bundle)... though the FluxEngine is a DIY "solder a connector or some pin header onto an FPGA dev board and flash it using Windows software" project and the dev board is suffering from the chip shortage. There's a Purchase a Greaseweazle page on the GitHub project's wiki and I managed to get a bare Greaseweazle V4, delivered, for about $36 Canadian.
I haven't had trouble finding "tested working" used 3.5" floppy drives on eBay to plug into my KryoFlux and Greaseweazle for under $30 Canadian including shipping from Europe.
fdformat& co. – Stephen Kitt Oct 24 '22 at 07:52fdformatwould require OS drivers that make the hardware available as a floppy block device, and to my knowledge these only exist for hardware on old-computers. So if that is the most important point of the question, the answer is "you need to write linux drivers for the hardware supported on modern computers". So then it's not about "which hardware", but "find someone with the skills to write a driver". – dirkt Oct 24 '22 at 11:50fdformatcommands with nonstandard sectors per track. I don't see the problem. – Joshua Oct 24 '22 at 14:46fdformatman page explicitly says “This utility does not handle USB floppy disk drives. Use ufiformat(8) instead.”fdformatrelies onioctls which aren’t supported by the USB floppy driver. – Stephen Kitt Oct 24 '22 at 15:21floppydriver if it had the same major/minor... I’ve never heard of a USB floppy that could be driven by thefloppydriver, I’d love to know more about it. (“Standard” USB floppy drives show up as SCSI devices, e.g./dev/sddon my system right now, and not as any of the/dev/fd…devices.) – Stephen Kitt Oct 24 '22 at 16:27