The question here is whether you are allowed to publish the results of your reverse engineering and decompilation efforts on GitHub. In this case, the answer seems like a very clear and obvious "no".
1. It's a derivative work of the original.
2. It's the entire executable, not just a portion.
3. It's not transformative.
4. The original work is creative.
5. It competes with demand for the original work (remasters).
With so many different factors stacked against it, I just don't see any kind of plausible defense here.
> Transcribing a play, you would get back an almost exact copy of the source material, whereas decompiling is more akin to taking a car and measuring all the bits of it.
Another red herring here... it is irrelevant how superficially close this is to the original source code.
When you compile a program, the result is not a copy of the original source code either. However, the compiled version of a program retains the copyright of the original source code. Likewise, a decompiled program would retain the copyright.
> The questions is wether there are enough legal loopholes to squash these generally allowed uses...
"Legal loopholes" kind of presumes that this sort of effort is permitted by default, but might be illegal through some kind of technicality. These people are distributing the results of IDA Pro / Ghidra decompilation efforts of an entire executable program on GitHub. Seems like very crystal-clear case of copyright infringement.
Again, to clarify things because people are hung up on this point--it is not about whether reverse engineering is legal. It is about whether you are permitted to distribute the results of reverse engineering. Kind of like asking whether it's legal to rip a CD... yes, ripping a CD is legal. Posting a ripped CD online is not.