Can two corporations avoid being 'associated' just by having different shareholders on paper?

No, not reliably. CRA and the associated corporation rules look at actual control and the real relationships between the people involved, including specific deeming provisions covering related persons and groups of people who act together, rather than stopping at whoever happens to be listed as a shareholder on paper. Simply putting different names on the shareholder registry for two corporations that are, in substance, still controlled by the same person, family, or closely connected group doesn't defeat association if the underlying relationships meet the statutory tests.

The rules were specifically designed with this kind of paper restructuring in mind, since using nominal or related shareholders to multiply access to the small business rate is exactly the outcome the associated corporation regime exists to prevent. An arrangement that looks, on its face, like two independently owned corporations can still be found associated once CRA examines who's actually calling the shots and how the relationships and financial interests genuinely connect.

Because attempts to sidestep association through shareholder arrangements that don't reflect genuine independent control are a recognized risk area, and can also draw broader anti-avoidance scrutiny in more aggressive cases, getting proper advice on a structure meant to avoid association is far safer than assuming a paper change alone will hold up.