My statement that gliitch quoted in the OP was a response to a PM not quoted here. The numbers given may be wrong, but the general idea may still be right.
In the meantime, gliitch has sent me a few sample save files (thanks!), and I have taken a look at them. Those save files have been created by different means, but belong to the same game (seemingly Phantasy Star 3 - Generations Of Doom).
1.
From "everdrive":
I guess this file has been created playing the game using an Everdrive plugged into a MegaDrive, and retrieved by reading the Everdrive's storage media with a regular card reader. Hence there was no interference from the Retrode.
@gliitch: Is that correct?
The file size is 12 kiB, but the first of every two bytes has the value FF. Removing those FF bytes yields 6 kiB of data resembling the other save files provided:
* 2 kiB savegame.
* 2 kiB unused memory (all FF).
* 2 kiB savegame identical to the first one -
@gliitch: Did you store the same game in two slots (I'd have), or might this be some kind of mirror?
Note: I guess that this is followed by another 2 kiB of unused memory, for a total of 8 kiB of memory, but the Everdrive truncates the file to the size that is actually used.
2.
From "megadrive":
I guess this file has been created using the original game cartridge in a MegaDrive, and retrieved using the Retrode.
@gliitch: Is that correct?
The file size is 16 kiB
minus 1 byte (why?). The data structure is:
* 2 kiB savegame.
* 2 kiB unused memory "A" (filled with alternating patterns of FF FF ... 00 00 ... disturbed by very few different, "random" values).
* 2 kiB savegame (identical).
* 2 kiB unused memory "B" (like above, but the "random" values and their locations are different).
* 2 kiB savegame (identical).
* 2 kiB unused memory identical to "A".
* 2 kiB savegame (identical).
* 2 kiB - 1 byte unused memory identical to "B", except that the last byte is missing.
3.
From "retrode":
I guess this file has been created using an emulator (Kega Fusion), the Retrode, and the original game cartridge.
@gliitch: Is that correct?
The file size is 16 kiB minus 1 byte. The data structure is:
* 8 kiB filled with alternating patterns of FF FF ... 00 00 ... disturbed by very few different values.
* 8 kiB - 1 byte identical to the first 8 kiB, except that the last byte is missing.
So, compared to the "megadrive" file, the "retrode" file has a similar structure, but the save slots seem to be empty.
Based on the above, my current, still flawed theory is:The game has 8 kiB of memory used for two save slots. Or maybe four save slots, and gliitch likes to use only the first and third of them, for a game and a backup copy.

Or the game itself duplicates the save slot(s) because there is such an abundance of memory, and if one copy is corrupted, the other may still be valid.
For some reason, the Retrode presents a 16 kiB save file. The first 8 kiB (16 sectors) of the file are mapped to the save memory as intended. But when the Retrode tries to access the nonexistent second 8 kiB of memory, the cartridge ignores the highest 1-bit of the address and again returns (when reading) or modifies (when writing) the data in the first 8 kiB. So the second 8 kiB of the file are mapped to the same memory as the first ("mirror").
See also my statement in the OP, with 32 kiB / 12 kiB replaced by 16 kiB / 6 or 8 kiB.
The flaw in this theory is: Above, gliitch said that the Retrode "wipes out" the save, replacing it with a "blank" one (like 3. above). But in my theory, the save should only be reverted to its previous state, not vanish completely.
This would be consistent if the "previous state"
was "blank", but I have no idea how gliitch could have created such a state after playing the game on the MegaDrive. Note the imperfect FF FF ... 00 00 ... patterns: if the game had intentionally cleared the slots, it would likely have filled them with all 00 (or all FF) instead.
I don't think that the battery is dead, because gliitch would likely have noticed that, and creating the "megadrive" file (2. above) would have failed then.
I don't know how the transition from "console power" to "battery power" works (or if there is a transition at all), but maybe the Retrode is controlling it wrongly, causing a short blackout in the save RAM.
Any ideas / comments?