Well, in the AF3 fight Ulbrecht was wielding a Blood-red Grimoire. And All-Seeing is a NM, which generally play by different rules.
But if you wanted to make a Stratagem that makes nukes AoE, you could simply have it so it has a significant damage reduction. Manifestation doubles cost and cast time, hypothetically you could just slap "halves damage" on it too and go with that (a real number would need to be tested, I doubt halving damage would be at all balanced).

Just to amend my Tabula Rasa suggestion now that I've been reminded, in the AF3 fight once Ulbrecht used Tabula Rasa his Stratagems would not wear off. That seems like a much better solution to my issue than just having all of them active when under the effect of it.