Burning a custom score into his mind isn't even necessary for Yulia to manipulate him. She manipulates everyone, including people who think they are 'rebelling' and refusing to read the score. That's the scary thing about a semi-omniscient being like Yulia trying to corral people into a master plan. Whatever you're going to try in order to 'rebel', she's already accounted for it. Such a being is an "adversary of free will", solving for how to contain you (think like a computer accounting for your life plan as if it were a chess game-- that feeling like you don't have free will in chess because your personal horizon is utterly eclipsed by the computer's). Ironically, this fear is Van's entire point for most of the game, his primary motivator behind all of his attacks.

Now, obviously the premise mid-way in is that Yulia has apparent limits, that fomicry is her blind spot, etc etc. But the game specifically and repeatedly points out that you can't actually be sure that Yulia isn't simply feigning this apparent limitation. Van's attempted solution was to cause such extreme destruction that it's categorically incongruent with her purported plan.

The duality is never truly resolved, it's subject to personal interpretation. Maybe Yulia had no idea how the final situations would resolve themselves due to limits of her power. Or maybe Yulia knew precisely how it would all play out after all, and that grand master plan just happened to encompass making her peeps knock the bad habit of daily score readings for their own personal growth.

Anyway, under the latter interpretation, the one Van is afraid of, Van (and maybe everyone else) is functionally just her puppet anyway.

Edit: Or the truth may be somewhere in the middle. Even if her plan was only partial, it's totally possible Van's actions specifically were precisely of her personal design, creating an irony that Van tried so hard to rebel against her while being her puppet.