I use Fuse and have uploaded/downloaded quite a few characters to Mixamo.
By the sounds of what you are doing, the website approximates bones placement on their custom algorithm, which is due to where you place the joints (Wrists, knees groin and chin)
This means that each time you rig something it may not be the EXACT outcome as it was the first time, bones will be out of place, Etc.
I don’t know if Fuse is the best answer to what you’re trying to accomplish, unfortunately. 