Thanks a lot for the follow up. I managed to find a similar thread with right this problem and explanation:
2017 to 2009 6MT Diff Swap - Install Notes
Apparently newer model Z's have these threads reversed. It is *never* threaded on both sides, only one side needs to be threaded and this is why the bolts will always have 3/4 threads, not full.
So old Z models:
Flange hole, half-axle threaded.
Newer Z's:
Flange threaded, half-axle hole.
Happy to know the whole issue now. So I will definitely drill the thread in the halfaxle and use the new thread in the flange and that's that.