Alright. So: I think this has been an issue since the existence of this software, and for some reason it has never been addressed or fixed.
Everytime an .FBX file with an armature is imported in the program, Blender removes the first bone in the hierarchy (which, in 90% of the cases, is a root bone, so a very important bone in the armature), and instead, it just makes its name the name of the armature.
In order to fix this issue, it is necessary to install an improved version of the FBX importer that can be found here: https://www.nexusmods.com/witcher3/mods/8105
But I find it quite ridicolous that this mod still needs to be used even with Blender 4.0+. FBX is a very common format that all of us use, why has this never been fixed?