I wouldn't recommend playing online with the mod installed. A lot of Pokemon have their hidden ability available as a regular ability, most learn egg moves by level up, and some are in different experience groups. All of these things will make them show up as illegal online, though you could edit them quickly in PKHex to make them legal. The legal version just means that all the in game trainers will have legal Pokemon, not that the Pokemon you catch will be legal for online play.
The new version of the hack is up now, enjoy!
EDIT: the mod also doesn't completely work with the 1.5 update for XY, so it can't go online without sacrificing a few features.