Key sectors containing things like the Partition Table, or a bootsector (Boot Record) are also supposed to be ones that do not change whether or not there is an OS (or any files) in the filesystem or not.
Break that down a little bit, a partition table should not change whether or not the partition(s) are formatted or completely blank. Not supposed to matter whether you are going to use the partition for DOS, Windows, Linux or whatever.
Then a bootsector doesn't even exist until its partition is formatted to begin with, then it reflects the "geometry" that the formatting process seemed to think was best for that filesystem based on the information it had available.
Neither of these should change after that, and be completely independent of whether there are any files in the filesystem.
It's probably best to build on as firm a foundation completely consistent with regular old PC's and it really looks like this is going pretty well using FAT16.
Once you have copied the IMG to a SSD, you could look at either IMG or hardware in DMDE and see the same thing. You do have to kind of figure I checked the IMG for potential bootability before I did anything on bare metal ;)
It is intriguing. There were other anticipated possibilities for an IMG to be bootable, like floppy mode or "large floppy" mode, which start with only a bootsector located at sector 0, no partition table is needed since there is never more than one partition.
Sector 0 right now is reminiscent of a FAT16 bootsector, looking at it in "FAT/FAT32/NTFS Boot Record" Mode, it displays real well. With FAT, you will see there are two different entries for Total Sectors.
By the time FAT16 came around, the upper Total had already been deprecated. You are using it for a full total of 65535 sectors which works so far but it should be in the lower Total Sectors entry for this template on FAT16. The upper entry should be 0 instead.
Then interestingly, looking at sector 0 in Partition Table mode, you do have a (un-needed at this time) partition table, in the usual position within the final bytes of sector 0. The 65535 total sectors are independently designated there (same total as above in the bootsector code that takes up the bulk of the bytes in sector 0 above) but there is no CHS geometry in place, and DMDE flags a "Relative Sector" of 0 as incorrect because it's expected to always be something other than 0. There's a number of structural features that can cause DMDE to flag them other than this too.
With sector 0 in DMDE you hit Editor > Partiton Table and all you're seeing interpreted is the last dozens of bytes of sector 0, it's only meaningful if there actually is a partition table in sector 0. There would be a maximum of 4 primary partitions in place. You can change this part all you want without having an effect on the code existing in the earlier bytes of sector 0 (such as an MBR ordinarily). But if you've got partitions the partition table better be sensible or it could fail to point directly to where the target code is.
No real partitions at this point so you can just go into Edit Mode and zero out the top primary partition line:
80 0E 0 0 0 0 0 0 0 65535
You have to hit File > Apply Changes. Then the partiton table is completely gone. And it will still boot just the same.
Random finding; there's a gfx_destory_window in sector 284 that looks like a typo.
Nothing in the OS should ever be hardcoded to rely on specific sectors, instead everything needs to be relative to the "Hidden Sectors" in the FAT which determine the offset which is the actual bootsector location for a primary partition.
The bootloader needs to be independent, and the OS itself needs to function regardless of what sector its partition starts on.