Megidolaon comes from Mitsuru's moveset as a boss in The Answer, which now that you mention it, she's still missing a couple of other abilities from. Gae Dearg and Rule Breaker are both more like dispels than drains. A better example of a draining NP would be
Ark, which, while obviously superior to Spirit Drain, explicitly drains magical energy and has a completely different effect than Rule Breaker.
Blood Fort Andromeda is another example of a mana draining NP working differently from Rule Breaker, though unlike Spirit Drain, it can be resisted. Spirit Drain is by no means an instant kill, but it allows Mitsuru herself to stay in the game indefinitely while directly attacking Berserker's mana supply, which could effectively be an alternate victory method for Mitsuru and is an instant K.O if and when Berserker runs out.
Sure, Raikou likely has great adaptability, but that's just another addition to her experience advantage, and isn't an actual counter to Mitsuru's healing. She still needs to finish off Mitsuru almost immediately or the damage will be annulled.
Almighty damage kinda doesn't care about Magic Resistance, and Weapon mastery is nice and all, but it doesn't really help when she needs to get close to use all but one of them, including the fire sword that's her only real shot of ending the fight quickly enough to overcome her opponent's healing. Angelic Grace counters Mana Burst by doubling Mitsuru's evasion rate against non-Almighty magic, and Sharp Student makes the Immediate killshot Raikou needs for victory all that much harder for her to feasibly hit.
Raikou will have to close the distance and struggle to land a single decisive blow, all the while she'll be getting constantly bombarded from afar with heavy unavoidable damage and potentially having her life force drained. Meanwhile Mitsuru can just fire off a few Megidolaons, adding Mind Charge if necessary, and not even have to worry about her own aim. She can focus all of her efforts on dodging what few ranged attacks Berserker actually has, healing herself on the
very unlikely chance she actually gets hit, and stealing Raikou's mana to sustain her own spells. And this is all assuming Raikou survives Megidolaon long enough to actually get close.