Shininess aside,
There's no 6IV Adamant PID (by Method 1).
It is known that in Gen 3 and 4, for anything generated by the existing Methods (typically non-eggs), if you want flawless IVs, your choice of nature is real limited.
If you want Adamant, it cannot be Flawless. So there's your initial problem right there: you wanted something impossible (to be legal)
[and IIRC, it has to be Method 1. Rayquaza in Gen 3 is Method 1]
No, those programs work fine. Once again, the problem is with what you wanted. (and maybe by extension, the problem was with you not knowing that not every non-egg's nature can be flawless )
It would be a nice QOL change, but ultimately unnecessary.
The other programs work just fine. If users can screw that up, then even if PKHeX were to import that functionality, users would screw it up on PKHeX too.
While potentially being true, coupled with my previous point, I would also imagine that it would be too much effort to bring such a change to life, when there are so many other things the devs can spend their time and effort on.
edit: anyhow, if your goal was to use it in Gen 7 or Gen 8, specific nature and perfect IVs isn't necessary.
Gen 7: Can Hyper Train
Gen 8: Nature Mint and Hyper Train :3