If you use https://www.psypokes.com/dex/hp.php to calculate the Hidden Power's strength, you get a value of 47. This is because the mentioned calculator isn't updated to Gen VI and thus doesn't assume a base power of 60. If you now use the calculator you linked to determine the damage dealt with a HP with a power of 47, you get the following results: 252+ SpA Magnezone Hidden Power Fire vs. 252 HP / 0 SpD Scizor: 272-324 (80.9 - 96.4%) -- guaranteed 2HKO
As you can see, Magnezone can't onehit Scizor. Since your results seem to fit to the calculations I did, I assume that PRO still uses the old formula that gives HP a strength of 30-70 depending on the IVs instead of a base power of 60. It's another one of those cases where PRO isn't quite up-to-date; another example would be Mamoswine which isn't able to learn Icicle Crash (A move it can learn in the actual games since Gen V)