Here's why I think the evil tadpole and the evil playthrough are linked and can't be seen as separate stories. And perhaps this could be made clearer for people who approaching this as new video game and not as a successor to the BG story. To me it seem connected because I have the Bhaalspawn story in mind.
The tadpole as Bhaal power analogue. Spoilers only to to avoid wall of text.
Bhaal's plan for his children was for them to be born with a seed of divine potential and, through many murderous acts, grow and nurture that divine spark. When the children had fully developed their potential they would clash and that part of their soul that was Bhaal's would return to his realm and provide fuel for his resurrection. The more you acted like papa Bhall, the more the seed would grow and the better the harvest. Sarevok had the idea that he could grow his seed but avoid the fall of the scythe.
(in the unpatched version of BG, the way to defeat Sarevok was to force him to fight on the Bhaal symbol where he would trip over all the traps. That's the ending still in the cinematic, Serevok blood filing the grooves of the Bhaal symbol. Even a good aligned 'Tav' ends up serving Bhaal's plan for Sarevok by performing a ritual sacrifice)
The cannon BG1 Tav realizes that she can grow her seed in a way that makes it useless for Bhaal's plan. If the seed is watered with acts of kindness and compassion instead of murder it grows into a form that is useless as resurrection fuel. The evil powers are more powerful than the "transformed" powers -- zero casting time Vampric Touch ftw -- but put you on the same path to ruin Sarevok walked down.
BG1 is about willpower vs destiny. In BG2 Tavs plans are disrupted and daddy Bhaal's plans are advanced even further. (I take the original plot, where Imoen is the final boss as the BG2 story) Willpower allowed you defeat the mage but your soul emerges worse for the wear.
Mellisan has a similar idea to Sarevok but she has the advantage of insider knowledge. She is going to raid Bhaal's granaries and use the Bhaal resurrection fuel to make herself a god.
So long story short, the motivation for an evil playthrough should the like that Sarevok and Mellisan. What if we could take the power but avoid the end? Don't remove the tadpole, control it. Find a way to use the Bhaal power for yourself, find a way to have the godlike powers of the absolute without becoming one of her slaves. Sure I'm wearing her brand, brandishing her shield, wearing her gloves and shouting her name but I have a card up my sleeve. Like Mellisan, I'm aware.
If I were to side with the goblins I as a sneaky neutral evil \ lawful evil PC I would be thinking "get in good with the real powers at moonrise towers, find out everthing I can about the Absolute and how I take her powers without becoming slave" To do this I want to impress that eye that is hovering near the drow not just Minthara herself.
And this should lead Tav down the road to ruin because that's just what happens in the FR.
From the original FR campaign setting:
"Finally, the Realms are a land of adventure, and therefore adventurers. It is the time of heroes, when one man of pure heart (or with a powerful artifact) may hold his own against enemy hordes, where legions of evil forces may muster and be destroyed by the actions of a few, where the nations rise and fall on magical tides which mere men can control."
Although I would note that Larian has chosen to assume that the cannon ending of Avernus is the failure of good. Zariel is alive and evil as ever.
