If you want a history lesson about fWNES, the FDS format (sort of), alternative Famicom Disk System file formats, the author/inventor FanWen YANG, that kinda thing, just ask -- I'm familiar with it a little bit because I'm one of the few (maybe the only?) people from the late 90s NES emulation/dev scene that spoke Mandarin. I did a history write-up but felt it wouldn't matter, but does go into Famicom disk formats prior to FDS (there are at least 3 I know of off the top of my head). Instead let's cut to it:
My view is the exact same as others stated here: what you have are technically disk images from a Game Doctor/Magicard unit from Bung. There are several Game Doctor-compatible copiers/units, all of which behave a little differently, no? Maybe they all use the same format, I don't know -- I don't have these devices. I do know that there are other companies that Bung who made such copiers (that's essentially what they are, particularly the later models), for example I think Venus Corp made one and strongly suspect Front Fareast had one. But there are also other systems that were used for dumping too -- if Donald Moore / MindRape was still with us, he'd love to talk about this -- like a particular model of Brother computer that could supposedly read Famicom disks.
The FDS file format is very clear: the per-disk-side size is 65500 bytes. And while bytes 5-15 of the 16-byte FDS header itself are all zero, they were intended to be used for mainly emulation purposes, e.g. "oh, we learned a new magical quirk about the FDS that happens only on some models, we need to use byte 5 for that purpose". If there IS something new/unique about the FDS itself that requires this data (i.e. is not Game Doctor/Magicard specific), then that's a different matter.
The FDS format is conceptually identical to the original NES format by Marat Fayzullin: much like the the 16KB PRG and 8KB CHR bank sizes of the NES format, this is another case of where the information available at the time (dumps, RE, pioneering efforts, etc.) made the best decision they could for that file format (FDS), and thus the 65500-byte-per-side definition. I know, lots of folks wish these formats had been more flexible size-wise, but they weren't. We must be pragmatic and err on the side of caution (read: ensuring full compatibility).
If that's not enough for you, here's a point to consider as a comparison:
There are many different SNES copiers from many companies, *all* of which use their own separate file format (sometimes not just a header!) and approaches, despite the ROM of the backed up game (obviously) being part of the image. You cannot take, for example, a .SMC/SWC file from a Super Wildcard and load it on a Game Doctor by simply changing the extension to .078. Conversion between these formats -- and there are *MANY* -- is commonly done with UCON
(I haven't used this version myself, but the early 90s DOS version was a godsend). And we've seen people come along and try to introduce new file formats due (only in part) to those annoyances, as well as only loading ROMs with those headers removed entirely (i.e. pure ROM images) -- nobody but the most pedantic of the pedants care, what came first (or thereabouts) "won the war".
Likewise, I strongly doubt you can take a Game Doctor/Magicard dump that's "oversized" like this and put it onto another device/copier/system (particularly one not from Bung) and have it work. You'd need a file conversion utility, or at least something that strips off the bytes between 65500 and whatever the byte before 0x01 + *NINTENDO-HVC*
was, to achieve a "raw" disk format. Heck, do you even know what those "oversized" bytes are for?
Game Doctor units apparently had all sorts of neat features (especially the later models); could it be data the unit itself reads/benefits from? If so, well then there you have it, that's a file format specific to those unit(s) and should be retained that way. So the fact remains that with a disk side larger than 65500 bytes means they're not compatible with the FDS file format as designed in the late 90s.
I would urge you to make your own file format with a different extension (maybe you can find out what Bung preferred these be named, extension-wise?), document that, and/or make a conversion utility that can strip off the unwanted bytes to convert to FDS (or maybe you could talk to the UCON folks and have them do it, considering they already support a boatload of NES-related file formats
, including one of the older Famicom disk formats I hinted at in my first paragraph).