After some time of analyzing and critical thinking I realized the answer was right in front of me the whole time and it just went over my head.
You see, war3map.j is technically a "fake" file meaning there's nothing important in it, it's just some default WE strings that get stored in .j script after you save the map in WE.
As for war3map.lua, I don't know which tools author used to protect the map and MPQ because even though most filenames are missing lua script is entirely intact and not obfuscated whatsoever, my only guess is perhaps because none of the known map optimizers are able to scramble Lua yet.
In any case I deduced lua script file was File00000321.xxx due to its size, the other bigger file 002.xxx is loading screen.
Also it's worth to mention this map was in fact written in TypeScript and then transpiled to Lua
Quote:
https://typescripttolua.github.io/
Quote:
https://github.com/cipherxof/wc3-ts-template
With all that out of the way I started looking for save system and stumbled upon this.

__TS__New is I believe some kind of object that seems to start before every trigger and PlayerSaveManager is trigger itself, subscribe should be equivalent to TriggerAddAction in Jass, I don't know what TriggerAddCondition would be.
Anyway, you don't need to know any of this in this case because all you have to do is change this line's flag and that will enable saving in SP.
Code:
self.saveLoad.disableSaving = true to false
After this, all you need to do is import lua script back to MPQ but since latest MPQ Editor can only open the map in Read Only, you need to use older version, I had luck with 3.6.0.854 version.
Unfortunately since we don't have a full listfile we can't flush the archive to reduce map file size so it will be slightly larger but that's the least of our concerns.
I have also made a small listfile that will search for correct path to war3map.lua so you don't have to look through the list of unknown filenames to find it.