Changing a player's ownership changes their Adjusted Ownership and, through it, changes their OLD Saber Score since adjusted ownership is a variable of the OLD Saber Score formula. It doesn't change regular Saber Score or Sim ROI.
In short, on its own, adjusting an ownership projection does not change anything about your lineups.
That's because Saber Score and Contest Sims don't use ownership numbers. They use field lineups, which are full sets of simulated opponent lineups. Saber Score runs against an internal field that can't be edited, so there's no way to make your ownership affect it. Sim ROI can use your ownership, but only if you build a field from it and point your Contest Sims at that field. The “How do I use my own ownership?” FAQ walks through all three steps.