It's so that noobs can level. The root of this problem isn't the eggs but the fact that Homunculii are not affected by lvl difference penalty. They can level from 1 to 99 in ant hell with ease because of this. If kRO fixed this then Alchemist would be forced to move for better exp and not stay in ant hell. Yes it will be much tougher to level Homunculii but it still is a semi free mercenary and gives +5% exp tap.
To do this they would make it so everyone whines about how OP homunculus is in WoE ETC... just try to take even a 99 homunculus to anywhere close to it's level range. You won't level there, period. They would either have to massively rework the stat progression and stat gain to scale with what a normal player could do or reduce the EXP needed / level on the homuncs by probably 60-75% or more. Thats the real reason you see homunulus in ant hell, go anywhere else with better EXP and they take so damn long to kill anything that people would be complaining about holding up spawn.... if you happen to have one that can even flee anything above level ~60+. If I wanted to tank for hour for someone else to kill a bunch of crap I would go find a random No0b in pront to help out....
Oh and since they pretty much share the merc codebase now, mercs would most likely be affected by the level penalty as well.... I doubt that would go over the greatest, it would probably be the final nail in the merc systems coffin.