That is intended to work that way, for an important reason: the bootloader is not just a mere bootloader, but installs complex code in memory and you don't know what it does. More on that: that code runs in a secure context, which is not accessible by anything, so you really don't know what it does and what it can do.
One clear example is the fact that the stock bootloader artificially blocks the rk3318 when it runs beyond 1.1ghz, while we have seen it is pretty capable of running at 1.3ghz perfectly fine like the rk3328.
The idea is to remove as much as possible of the proprietary blobs (ie: the stock bootloader) and provide open alternatives; tinkering with the bootloader may work now but surely will cause troubles when there will be an updated bootloader.
Your case with broken emmc is a different condition by the way, because you have limited alternatives. However there are no real secrets in the boot process, just some complexities and some of them are explained here
Then it would not be a maintenace tool anymore but something else; but feel free to take it as a base for anything else!
Hint: speaking of Kodi, you are just heading on something like LibreElec
Yes, and also because it is the only what to make it cross-OS down to Windows XP.
Previously (four months ago) the partition was FAT32, but it would not support files larger than 4Gb