This is because by the game's data, they're different enemies. They have different stats, HP, resistances, they may look and act the same but as far as PSO is concerned, they're different entities. Changing the stats of the ep2 enemies to be in like with their ep1 versions or vise-versa would defeat the purpose. Also the EVP of enemies in ep2 is higher than those of ep1, so if anything it balances out a bit.
They don't need to remove the Dark Flow entirely. If you compare the stats of DF on the server to those of it logged on PSO World you'll see that Ultima boosts the ATP to 400%. DF was powerful enough when it got combo-unlocked. They either need to remove its combo ability, or reduce ATP back down to normal. (DM would follow suit as well.) But I agree, luckily people are usually chill about not using the special. (Except this one guy I met in-game, Scott7 or something.)
The game is supposed to be easy at that high of a level because it's supposed to take you ages to get to that kind of level. But that would involve going off on another rant. Instead impose challenges on yourself because a 5th difficulty is virtually impossible, or at least too much work to get working.
Remove internet.