Since I tried making a WIP Mod of mine compatible with this one, I noticed that in the XComGameData_CharacterData.ini for this Mod there is, well, this:

[XComGame.X2Character_DefaultCharacters]
[MutonM2 X2CharacterTemplate]
[...]
+CharacterBaseStats[eStat_FlankingCritChance]=100

while you gave
[MutonM2_Diff_1 X2CharacterTemplate]
+CharacterBaseStats[eStat_FlankingCritChance]=33
[MutonM2_Diff_2 X2CharacterTemplate]
+CharacterBaseStats[eStat_FlankingCritChance]=40
[MutonM2_Diff_3 X2CharacterTemplate]
+CharacterBaseStats[eStat_FlankingCritChance]=40

(pretty self-explanatory)

I noticed that
[MutonM2_Diff_0 X2CharacterTemplate]
is missing which could have contained the alternate stats for those Centurions on Rookie (not that that many like these templates exist, there is only one, for XCOM Soliders). To fix it, it is obvious to simply adjust the 100 (and hence why only one of Diff_0 exists).

So I tested it ingame just to make sure, luckily I still had 10xHP and Damage for all vanilla troops (not just XCOM) so I could endure all these Melee attacks, War Cries and Suppression on my deliberately exposed units in the first mission where I simply replaced the ADVENT troops and indeed, they always landed a critical hit.

In any event I am still happy that this appears to be the sole little bug, so I'd still like to mention on a side note that you did a good job and oh boy, I also had enough opportunities to "study" the model and textures :3