I am pretty sure that modifying the henchmen manually with Leto will work, in the sense that it won't break the game and the henchmen will have whatever level features you give it that way. However, that may mean that you will essentially have to do it for every level up, since it doesn't change the leveling priorities in the level-up package and the LevelUpHenchman() function will still try to use a package even if you have previously made choices for which the package priorities aren't appropriate.
This topic comes up often enough that I wonder if there aren't more packages available for the various classes (or at least for the standard henchmen) available on the Vault. For instance, I am pretty sure that Tony K's AI levels the henchmen differently than the default game does, but I don't know if it does that using new packages (it doesn't for the OC, I'm pretty sure, since the OC doesn't use that package system).