I’m not really sure why any one would be baffled. All the reputations have worked like this. In Legion we more or less had access to all the same factions so unlocks were fairly straightforward. In BfA we went back to the Alliance and Horde split.
Mechagon is a neutral faction. Just like Argussian reach and Army of the light were. There was no big outcry then when we could unlock the Void Elves and Nightborne regardless of what faction our character was on. Why would this be any different.