You've to have an absolutely madcap of a character to go around collecting tad-poles and inserting them into their head. You can't make this stuff up. I was willing to accept the change to the lore of ceremorphosis in order for the story hook, but one needs to draw the line somewhere. I'd like to think the system is there for those who care nothing for the overall narrative, but I can't imagine Larian will place too much malus on the player that utilizes their tad-pole mini-game. As they themselves saw it as a necessary sub-system for player customization given the size of the game relative to the level cap they decided on.
As far as balance between those that partake and those that don't, I can't imagine they even care about that. All their supposed 'balancing' simply unbalances other parts of the system, as far as I can tell. These last few 'reveals' have made me more apprehensive about the game than ever before. If nothing else, I think this game is going to be absolutely hilarious.